Help! messed up renders in timeline

(I'm reposting because no one has yet responded and I'm on a deadline...)
I'm having a strange problem with FCP 6.0.3 : Footage looks fine in the timeline during editing but, after a render of "green" preview clips, the rendered clips show the wrong parts (i.e. FCP seems confused about the timecode). If I un-render those clips, the footage is okay again.
My timeline is DVCProHD but mixes footage of various formats. The problems appear to be only in non-DVCProHD footage that needs to be rendered (i.e. DV, HDV, and Apple Intermediate Codec). Also, when I pasted part of an older sequence into my new timelines, some clips are displaying in the wrong aspect ratio, and FCP has added small gaps to other parts of the timeline (i.e missing frames).
Can anyone help??
I thought it may be corrupt preferences, so I ran FCP Rescue 6, but no luck.
Thanks!
-J.
-J.

Thanks Michael.
Compiling this list, I realize I may be going for a new record for mixing formats -- live action HD and DV plus various types of screen capture footage. I have been scaling all the footage up to the sequence size.
If you have a solution for re-compressing the problem footage into a high quality format (that would not lose image quality), please let me know codec and software so I can run more tests.
My sequence settings are:
Vid Rate: 23.98 fps
Frame size: 960x720
Compressor: DVCProHD 720p60
Pixel aspect: HD (960x720)
Audio Rate: 48.0 KHz
+ + +
Problem clips #1: renders pull wrong time codes
AIC (Apple Intermediate Codec)
25 fps
1280x720
Square pixels
Data rate: 3.3 MB/sec
[Failed test1: I recompressed a Problem Clip #1 into HDV 720p30 and renders are still incorrect]
[Failed test2:
I recompressed a Problem Clip #1 into DVCProHD 720p60 and renders are still incorrect]
Problem clips #2: renders are improperly scaled (but are correct in sequence)
HDV 720p30
15fps
720x480
Data rate: 1.1MB/sec
Field dominance: lower
Audio rate: 44.1 KHz
[Successful test: I recompressed a Problem Clip #2 into DVCProHD 720p60 and the render time code is now correct, however the clip is noticeably softer]
Problem Clips #3: renders pull wrong timecode
HDV 720p30
1280x720
Vid rate: 8fps
square pixels
+ + +
Okay clips #1:
DVCProHD 720p60
23.98 fps
Data rate: 5.9 MB/sec
Pixel Aspect: HD (960x720)
Okay clips #2
DV / NTSC
29.97 fps
Okay clips #3:
AIC
15 fps
Data rate: 199.8 kps
864x486
Okay clips #4:
HDV 720p30
Vid rate: 4fps
Frame: 891x493
Square pixels
Date rate: 333 kps
Field dominance: none
Okay clips#5:
Compressor: Fraps (Perian)
30fps
Data rate: 14.4 MB/sec
1440x852
Square pixels
+ + +
Clips are stored on external G-RAIDs. It seems many of the problem clips are actually on a different G-RAID than the other footage (could that make a difference?). However, other media stored on this drive (DVCProHD and AVI format) renders correctly.

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