Making cross-platform AVIs readable by Windows?

Okay, before describing the whole problem, we're using Compressor 2.0.1 Academic, not 2.3 as we have G5 Macs here and didn't feel the need to do the crossgrade upgrade, and I don't necessarily need a Compressor based solution, just any solution that works. (if not Compressor, then hopefully some freeware app)
Basically, I need to get cross-platform AVIs that are readable by Windows, of finished projects, that can then be converted into WMV format with Windows Media Encoder. I'm aware of solutions like Flip4Mac and Cleaner, but I don't want to limit myself to WMV7 support, and Flip4Mac doesn't give advanced enough options in terms of setting things like bitrate.
I've tried a variety of tools, including Compressor, MPEG Streamclip, ffMpegX, and I just can't get cross-platform readable AVIs, either in uncompressed format, or using Apple Motion-JPEG at 100% quality.
The main problem with Compressor, at least 2.0.1 (if they've fixed it in 2.3 please let me know), is that once an AVI gets above a certain file size, it seems to be 4GB, but this isn't a FAT32 file system limitation, then the index header just gets corrupt.
That is, let's say I want to compress HDV to WMV. I have to:
a) Compress from HDV to a H.264 100% quality (or Apple Motion-JPEG 100%) RESIZED to 960x540. (half size) This is because Compressor can't resize files going to AVI
b) then compress that file to an uncompressed AVI
c) drag that AVI into VirtualDub on a PC, which will read it, but has to reindex the file, and then output another uncompressed copy
This does work, but it's cumbersome as ****, and there has to be a better solution.
The guys at Squared5 (MPEGStreamclip) said 1.8 fixed the problem with AVI's not being cross-platform readable, but I tried that version, and I'm getting errors, so I've sent them error logs to try and troubleshoot it. The error log in question is here:
http://www.goodcowfilms.com/web/mpegstreamclip18errorlog.rtf
ffMpegX will kinda work, if I use the Microsoft MPEG4v2 codec, but only up to a certain filesize as well.
DivX Pro won't take HDV files, so that isn't helpful.
Any suggestions here? I just need to make AVIs, in a lossless (or near close, like 100% JPEG) format that are cross-platform compatible.
Thanks in advance.
work: 4x2.5GHz G5, 4GB DDR2 SDRAM/home: 1.83GHz Core Duo, 1GB 667MHz DDR2 SDRAM   Mac OS X (10.4.8)  

How new is the version you speak of? I tried the demo for their highest end WMV suite about a month ago, and not only did it not allow you to set custom bitrates, but when converting video it left a green tinge on it that would come and go. (HDV to WMV)
I also apparently found out the exact feature or support I need... I need a Mac program that can write an AVI 2.0 complaint file. AVI 1.0 doesn't support files over 4GB, whereas AVI 2.0 has an unlimited file size limit.
Squared5, the makers of MPEGStreamclip, are going to look into adding it into their next version.
work: 4x2.5GHz G5, 4GB DDR2 SDRAM/home: 1.83GHz Core Duo, 1GB 667MHz DDR2 SDRAM Mac OS X (10.4.8)

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