Audio out of sync after media managing?

Hey! I have an interesting blip in the software found after I media managed a project of mine. Here is how I media managed the program:
Copy media referenced by duplicated items
Include render files
Include master clips outide selectin
Delete unused media from duplicated items
Use handles of 1 sec.
Include afiliate clips outside selection
Base media file names on exisiting names
Duplicate selected items and place in a new project but not including nonactive multiclip angles.
and I ended up getting something really interesting.
On some of my media clips, the audio associated with it had small blue bars across the top of each of the two audio channels. When an audio clip had one of these bars more often than not it only started halfway down the clip. At that point, when playing the clip from the beginning the audio would restart from the beginning of the clip again. It looks scary at first, but all that I did was control click (right click) on the clip and "remove attributes." We don't have any affects associated with these clips so nothing under the Remove Attributes box was checked, but I just clicked "OK" which seemed to effectivly refresh the clip and the audio was perfect again.
So, I'm wondering why it did this, and what I can do to avoid it doing this in the future. I'm about ready to move on to a new job and would like to figure out how to avoid it or know if I need to write up a little something for the next person in this position to know how to deal with it and not to freak out!
Thanks!
Heather

>Frame rate mode                  : Variable
No version of Premiere does "well" with Variable Frame Rate
Below is about iphone, but may help
Some people find that Iphone won't edit easily because it uses a variable frame rate
- A possible fix in message #22 http://forums.adobe.com/thread/934466

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    ============================================================
    General
    Complete name                    : /Users/jukeboxhero/20140203.mov
    Format                           : MPEG-4
    Format profile                   : QuickTime
    Codec ID                         : qt 
    File size                        : 638 MiB
    Duration                         : 34mn 46s
    Overall bit rate                 : 2 566 Kbps
    Encoded date                     : UTC 2014-02-04 06:52:45
    Tagged date                      : UTC 2014-02-06 15:55:40
    Writing library                  : Apple QuickTime
    Video
    ID                               : 2
    Format                           : AVC
    Format/Info                      : Advanced Video Codec
    Format profile                   : [email protected]
    Format settings, CABAC           : No
    Format settings, ReFrames        : 2 frames
    Format settings, GOP             : M=2, N=30
    Codec ID                         : avc1
    Codec ID/Info                    : Advanced Video Coding
    Duration                         : 34mn 46s
    Bit rate mode                    : Variable
    Bit rate                         : 2 449 Kbps
    Width                            : 1 920 pixels
    Height                           : 1 080 pixels
    Display aspect ratio             : 16:9
    Frame rate mode                  : Variable
    Frame rate                       : 18.969 fps
    Minimum frame rate               : 6.522 fps
    Maximum frame rate               : 19.355 fps
    Color space                      : YUV
    Chroma subsampling               : 4:2:0
    Bit depth                        : 8 bits
    Scan type                        : Progressive
    Bits/(Pixel*Frame)               : 0.062
    Stream size                      : 609 MiB (95%)
    Language                         : English
    Encoded date                     : UTC 2014-02-04 06:52:46
    Tagged date                      : UTC 2014-02-04 15:27:35
    Color primaries                  : BT.709-5, BT.1361, IEC 61966-2-4, SMPTE RP177
    Transfer characteristics         : BT.709-5, BT.1361
    Matrix coefficients              : BT.709-5, BT.1361, IEC 61966-2-4 709, SMPTE RP177
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    ID                               : 1
    Format                           : AAC
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    Codec ID                         : 40
    Duration                         : 34mn 45s
    Bit rate mode                    : Constant
    Bit rate                         : 104 Kbps
    Nominal bit rate                 : 128 Kbps
    Channel(s)                       : 2 channels
    Channel positions                : Front: L R
    Sampling rate                    : 44.1 KHz
    Compression mode                 : Lossy
    Stream size                      : 25.9 MiB (4%)
    Language                         : English
    Encoded date                     : UTC 2014-02-04 06:52:45
    Tagged date                      : UTC 2014-02-04 15:27:35
    ============================================================
    The video imports perfectly into Final Cut Pro 10.1.1
    I have Premiere Pro trial and Final Cut Pro trial. If there's no fix or easy work-around, I will have to ditch Premiere.

    >Frame rate mode                  : Variable
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    Below is about iphone, but may help
    Some people find that Iphone won't edit easily because it uses a variable frame rate
    - A possible fix in message #22 http://forums.adobe.com/thread/934466

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