MP4 files in CS5 twitching

Hello everyone. Not long ago I had problems using footage in CS4, which was discussed in this thread
http://forums.adobe.com/message/3805546?tstart=0
I was pointed to fact that CS5 handles MPEG files better than CS4 and I did find out that CS5 could play my footage without black bars or green frames which plagued me in last discussion. However, as I had chance using CS5 for this scene I though I'd just use it so I don't have to transcode every other file. Now I have another problem editing these files.
As I opened (and thus converted) my old CS4 project to CS5 I found that compositions didn't work the way they used to work. Files, mask and all were there, but footage didn't play the way it was supposed to. It looks like it plays frames in wrong order giving footage very twitchy look. For example frame 1, 3, 2, 5, 4, 7, 6 etc. Jumping back and forth. I though it was just messed up in converting process, so I tried starting from scratch, created new project, improrted same files and started doing composition all over. It looked like it worked, I previewed some of the files and saw no twitching. I finished comp 1 and moved to another one; twitching returned. I checked the one I had just finished and now it was twiching too.Interestingly enough, the files I had already ran through media encoder didn't twitch.
I can always move back to my own CS4 and run everything through media encoder, but I'd rather use the footage the way it is. Does this problem sound familiar to any of you? Something obvious I'm missing? I checked framerates and it all should match. It is very frustrating to face so many problems all of a sudden, I have never had problems like this with my camera or AE.
Thanks
*edit*
And while I'm at it, can you think of any way to define whether there is something wrong with my camera or is this (referring to older discussion) propably something AE related? I tried older footage with CS5 and it twitched all the same, but all old footage works fine with CS4, it's just the last two days of shooting that have caused problems.How propable is it that AE all a sudden decided to read these formats differently or something and still be able to use older footage of the same camera just fine?

There's a chance something's screwy with the camera. Settings may have changed without you knowing.
There's also a (better) chance that something is screwy with your computer.
What are your memory and multiprocessing settings? What are your computer's specs?

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Complete name                    : E:\tami\video\M4H04540.MP4
Format                           : MPEG-4
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Codec ID                         : MSNV
File size                        : 17.5 MiB
Duration                         : 16s 16ms
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Encoded date                     : UTC 2011-07-01 07:14:25
Tagged date                      : UTC 2011-07-01 07:14:40
Video
ID                               : 1
Format                           : MPEG-4 Visual
Format profile                   : Advanced Coding Efficiency@L4
Format settings, BVOP            : Yes
Format settings, QPel            : No
Format settings, GMC             : No warppoints
Format settings, Matrix          : Default (H.263)
Codec ID                         : 20
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Width                            : 1 280 pixels
Height                           : 720 pixels
Display aspect ratio             : 16:9
Frame rate mode                  : Constant
Frame rate                       : 29.970 fps
Color space                      : YUV
Bit depth                        : 8 bits
Scan type                        : Progressive
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Bits/(Pixel*Frame)               : 0.326
Stream size                      : 17.4 MiB (99%)
Encoded date                     : UTC 2011-07-01 07:14:25
Tagged date                      : UTC 2011-07-01 07:14:40
Audio
ID                               : 2
Format                           : AAC
Format/Info                      : Advanced Audio Codec
Format profile                   : LC
Codec ID                         : 40
Duration                         : 16s 0ms
Bit rate mode                    : Constant
Bit rate                         : 64.0 Kbps
Channel(s)                       : 1 channel
Channel positions                : Front: C
Sampling rate                    : 24.0 KHz
Compression mode                 : Lossy
Stream size                      : 125 KiB (1%)
Encoded date                     : UTC 2011-07-01 07:14:25
Tagged date                      : UTC 2011-07-01 07:14:40
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