Four corrupted frame in video

I'm trying to create a time lapse of 1170 images I took during the Geminid meteor shower.  I edited all the files in Lightroom v4.3 with the Catalog Settings set to "Automatically write changes into XMP" selected.  Lightroom created all the necessary XMP files for each CR2 file.  All the files look great in Lightroom.  After importing them into After Effects v11.0.2.12, there are four frames that are corrupt, although this varies.  Two of the frames appear really dark.  It's as though the Blacks got set extremely negative (e.g. -100).  The other two frames look like color calibration charts.  Here are the changes I made in Lightroom:
White Balance:
     Temp    3600
     Tint     -18
Tone:
     Highlights     -74
     Whites          +21
     Blacks           -10
Presence:
     Clarity          +10
     Vibrance       +20
Tone Curve:
     Medium Contrast
Sharpening:
     Amount     30
     Radius       1.2
     Detail        35
     Masking    10
Noise Reduction:
     Luminance     15
     Detail             65
     Contrast         30
Lens Correction
     Enabled with Default settings
First, is there a way to find out which filename (e.g. _S1P8449.CR2) is associated with a particular frame?  When importing into AE, I selected all necessary files at once ensuring the Camera RAW Sequence was checked.  There were two frames missing but it indicated a range from 8282-9453. When I render or do a memory preview, I seem to always get bad frames.  In addition, they seem to be random.  One time through, it was frames 356, 398, 816, and 921.  The next time through, after purging the cache and memory, it was 460, 496, 727, and 1017.  It's been very frustrating trying to figure out what's going on.  I've tried rendering as Quicktime, FLV and AVI just to name a few.  They all show these corrupted files.  I even tried using the standalone Adobe Media Encoder for rendering.  It too had the bad frames.  Any help would be greatly appreciated.
I'm using Windows 7 with the latest service pack and all updates.  I have 24 GB of memory.  I have Adobe Master Collection CS6 with all the latest updates. 
Thanks,
Wade

Why not simply "preprocess/ batch" your pictures in LR , adjust them to comp size (maybe slightly larger), ++ ... and export them as jpegs to AE? Although RAW - or 16 bit TIFF's , as Mylennium suggestes,  retain the full quality of the image, these files are big, slow and in most instances an overkill IMHO . Lightly compressed JPEG files  lose very little quality and should be more than sufficient.. Post-adjustments on these files in AE is much better invested time and effort - at least for me  
http://progresit.com/nordlys8.html --  timelapse example here 

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    * @(#)FrameAccess.java 1.5 01/03/13
    * Copyright (c) 1999-2001 Sun Microsystems, Inc. All Rights Reserved.
    * Sun grants you ("Licensee") a non-exclusive, royalty free, license to use,
    * modify and redistribute this software in source and binary code form,
    * provided that i) this copyright notice and license appear on all copies of
    * the software; and ii) Licensee does not utilize the software in a manner
    * which is disparaging to Sun.
    * This software is provided "AS IS," without a warranty of any kind. ALL
    * EXPRESS OR IMPLIED CONDITIONS, REPRESENTATIONS AND WARRANTIES, INCLUDING ANY
    * IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE OR
    * NON-INFRINGEMENT, ARE HEREBY EXCLUDED. SUN AND ITS LICENSORS SHALL NOT BE
    * LIABLE FOR ANY DAMAGES SUFFERED BY LICENSEE AS A RESULT OF USING, MODIFYING
    * OR DISTRIBUTING THE SOFTWARE OR ITS DERIVATIVES. IN NO EVENT WILL SUN OR ITS
    * LICENSORS BE LIABLE FOR ANY LOST REVENUE, PROFIT OR DATA, OR FOR DIRECT,
    * INDIRECT, SPECIAL, CONSEQUENTIAL, INCIDENTAL OR PUNITIVE DAMAGES, HOWEVER
    * CAUSED AND REGARDLESS OF THE THEORY OF LIABILITY, ARISING OUT OF THE USE OF
    * OR INABILITY TO USE SOFTWARE, EVEN IF SUN HAS BEEN ADVISED OF THE
    * POSSIBILITY OF SUCH DAMAGES.
    * This software is not designed or intended for use in on-line control of
    * aircraft, air traffic, aircraft navigation or aircraft communications; or in
    * the design, construction, operation or maintenance of any nuclear
    * facility. Licensee represents and warrants that it will not use or
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    import javax.imageio.*;
    import javax.imageio.stream.*;
    import java.awt.image.*;
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              System.err.println("Video format: " + videoFormat);
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              try {
                   Codec codec[] = { new PostAccessCodec(videoSize)};
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              p.prefetch();
              if (!waitForState(Processor.Prefetched)) {
                   System.err.println("Failed to realise the processor.");
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         public Dimension parseVideoSize(String videoSize){
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                   y = Integer.parseInt(sizeStrtok.nextToken());
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                   prUsage();
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                   // For demo, we'll just print out the frame #, time &
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                             + frame.getSequenceNumber()
                             + ", time: "
                             + ((float) t) / 100f
                             + ", len: "
                             + frame.getLength());
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              // We'll advertize as supporting all video formats.
              protected Format supportedIns[] = new Format[] { new VideoFormat(null)};
              // We'll advertize as supporting all video formats.
              protected Format supportedOuts[] = new Format[] { new VideoFormat(null)};
              Format input = null, output = null;
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                   return "Pre-Access Codec";
              //these dont do anything
              public void open() {}
              public void close() {}
              public void reset() {}
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                   return supportedIns;
              public Format[] getSupportedOutputFormats(Format in) {
                   if (in == null)
                        return supportedOuts;
                   else {
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                        // as the output since we are not modifying the bit stream
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                        Format outs[] = new Format[1];
                        outs[0] = in;
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                   input = format;
                   return input;
              public Format setOutputFormat(Format format) {
                   output = format;
                   return output;
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                   accessFrame(in);
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                   Object data = in.getData();
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                   out.setLength(in.getLength());
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                   return new Object[0];
              public Object getControl(String type) {
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                   supportedIns = new Format[] { new RGBFormat()};
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                             ImageWriter writer = (ImageWriter) writers.next();
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                             //writer.write(imagebi);
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                             + ", time: "
                             + ((float) t) / 100f
                             + ", len: "
                             + frame.getLength());
              public String getName() {
                   return "Post-Access Codec";
              private Dimension size;

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    Complete name                            : Y:\Live\2012-12-4 Farcry 3\2012-12-04_200413079.mp4
    Format                                   : MPEG-4
    Format profile                           : Base Media
    Codec ID                                 : isom
    File size                                : 4.33 GiB
    Duration                                 : 2h 11mn
    Overall bit rate                         : 4 713 Kbps
    Writing application                      : Lavf54.0.100
    Video
    ID                                       : 1
    Format                                   : AVC
    Format/Info                              : Advanced Video Codec
    Format profile                           : [email protected]
    Format settings, CABAC                   : Yes
    Format settings, ReFrames                : 4 frames
    Codec ID                                 : avc1
    Codec ID/Info                            : Advanced Video Coding
    Duration                                 : 2h 11mn
    Bit rate                                 : 4 574 Kbps
    Width                                    : 1 280 pixels
    Height                                   : 720 pixels
    Display aspect ratio                     : 16:9
    Frame rate mode                          : Variable
    Frame rate                               : 29.970 fps
    Minimum frame rate                       : 5.000 fps
    Maximum frame rate                       : 30.303 fps
    Color space                              : YUV
    Chroma subsampling                       : 4:2:0
    Bit depth                                : 8 bits
    Scan type                                : Progressive
    Bits/(Pixel*Frame)                       : 0.166
    Stream size                              : 4.20 GiB (97%)
    Writing library                          : x264 core 125 r2200 999b753
    Encoding settings                        : cabac=1 / ref=1 / deblock=1:0:0 / analyse=0x3:0x113 / me=hex / subme=2 / psy=1 / psy_rd=1.00:0.00 / mixed_ref=0 / me_range=16 / chroma_me=1 / trellis=0 / 8x8dct=1 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=0 / threads=18 / lookahead_threads=3 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 / bluray_compat=0 / constrained_intra=0 / bframes=3 / b_pyramid=2 / b_adapt=1 / b_bias=0 / direct=1 / weightb=1 / open_gop=0 / weightp=1 / keyint=250 / keyint_min=25 / scenecut=40 / intra_refresh=0 / rc_lookahead=10 / rc=crf / mbtree=1 / crf=13.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / vbv_maxrate=5000 / vbv_bufsize=7000 / crf_max=0.0 / nal_hrd=none / ip_ratio=1.40 / aq=1:1.00
    Audio
    ID                                       : 2
    Format                                   : AAC
    Format/Info                              : Advanced Audio Codec
    Format profile                           : LC
    Codec ID                                 : 40
    Duration                                 : 2h 11mn
    Bit rate mode                            : Constant
    Bit rate                                 : 128 Kbps
    Channel(s)                               : 2 channels
    Channel positions                        : Front: L R
    Sampling rate                            : 44.1 KHz
    Compression mode                         : Lossy
    Stream size                              : 120 MiB (3%)

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