Compressor 3.02 In and Out Points Not Correct

This is a follow up to my compressor truncating movies post. I'd like to reiterate that my workflow has not changed and no new software has been added to my system. This work flow used to work like a charm, however after the most recent pro applications update this bug surfaced.
If i drag and drop any uncompressed .mov into compressor, compressor incorrectly detects the in and out points for that clip and truncates the file on output. It seems to be by the same amount every time.
Example:
Clip 1 is a 320x240 uncompressed .mov file created and exported directly from final cut pro (exported as self-contained). the file is 1:53:32 in duration.
Drop that clip into compressor and it sets the in-point at 59:56:09 (it does this every time no matter what clip i try to compress...) and incorrectly reports the duration of the movie as 1:53:05. these in and out times and duration are found in the preview window. no in and out points are set in compressor.
this being said, the resulting output file (same size, same frame rate - no changes to timing) is truncated and the last 4 seconds and change are cropped off the end of the clip.
Any ideas? anybody else have the same kind of problem and find a fix?
I've trashed preferences to no avail... help!
karl

right - the question is... what do we do about it?
i have been able to narrow this down to a problem with footage that's 23.98 fps only however as this is part of my 24p workflow - and because it's the only reason i'm using fcp at this point -- in essence, this problem renders the entire final cut studio useless.
so frustrating!
who's found a workaround/fix for this?? i've been using this same workflow successfully for years and in previous versions of final cut. this problem only surfaced in the past couple of weeks.
AAARGH!
k

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Thanks for these suggestions. I'll try and answer each one:
Is the Source Monitor zoomed out to show the whole clip? If not, please zoom out to see if the In/Out points are getting painted in the wrong place initially.
Yes, it is zoomed out.
Do the clips have non-zero start timecode? If so, please try with a clip with zero-based timecode. (If you don't have one handy, you can create one fairly easily by exporting a sequence with start TC of 0;00)
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Compressor 3.02 In and Out Points Not Correct

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