Blocky Pixellated .M2T Import of clips trimmed in MPEG2VCR

Hi all,
I have a strange problem with CS3 that I was not experiencing with PPro 2.0. This is on a clean install/format/OS on a new machine, XP Pro, Quad Core Pentium, 2GB ram, two 500gb sata drives. (I tested and the same problem happens on my older machine, so it's not machine-specific.)
My workflow is I have many, many short .M2T clips 1080/60i from the Canon HV20. I can import these raw clips into CS3 fine, no problems. However, with most, I use Womble MPEG2VCR to first "trim" the clips and delete some unwanted footage at the beginning and end of each clip (and to save HDD space). This does not re-encode the clips, and I save the trimmed clips to a new TS file with the .M2T extension.
In PPro 2.0, these 'trimmed' M2Ts played perfectly and could be edited just fine on the timeline, adding transitions/effects/etc. alongside the 'raw' untrimmed M2Ts. However, now in CS3, when I import the MPEG2VCR trimmed clips, I get a 1st frame of all red, then after terrible pixellated and blocky playback, with some all red frames interspersed in there as well. I am just guessing, but it seems like CS3 has lost knowing where to find the I frames and is having a problem putting back together the sequence of IPB frames.
Strange thing is, if I save the trimmed clips as an MPEG Program Stream file (.MPG extension) in MPEG2VCR, those clips import and play perfectly in CS3. When I look at the properties of both files in CS3, all the details are exactly the same for both files (except size, the MPG file is just slightly smaller than the M2T version).
I know the obvious and slightly sarcastic answers to my problems :) -- just import as MPG! Or don't import M2Ts at all! Use an intermediary like Lagarith lossless AVI or Cineform! But I really don't want to do that, as I have thousands of M2Ts I need to import and don't want to convert all of them to AVI if it's not needed for my rather basic editing needs. And I'm concerned if I import some clips as M2T and some as MPG, if I then go to export the finished timeline as M2T there may be a problem. (I know probably not, but i'd feel safer keeping everything consistent as M2T for the importing).
So does anyone know how to fix this problem? I know I could go back to PPro 2.0 but I have a big investment in CS3 and I like its new features. Thanks guys (and gals) for your help in this forum.
Regards,
Patrick

Thanks Howard.
As another experiment, I tried trimming an M2T file in Womble MPEG Video Wizard DVD (their replacement for MPEG2VCR) and the trimmed clip again plays back pixellated in PPro CS3 but ok in other programs.
Rather than just throw in the towel and go back to 2.0, I'd really like to know the root cause of why this is happening, and why the files work ok in 2.0 but not in CS3. My understanding is that a TS file (transport stream) and MPG file (program stream) are identical except that the TS (M2T) file adds a few additional error correction bits for carriage of the signal over less reliable carriers, like broadcast. There must be something with those bits that are changed by trimming in MPEG2VCR, even though it is supposed to be a GOP-accurate editor, which other players can correct for but not CS3.

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