I have not had problems with CS6 for Windows and Venus 7000’s with uncompressed. HUFFYUV codec & WMV9 also seems to work well.
Daktronics older software seems to work fine with these using 6.05 through 6.10.
If you want to send me a sample file, I can help you analyze the codec and probably find a solution.
Choose uncompressed AVI from AfterEffects, or -vcodec rawvideo and -vcodec huffyuv seem to work well from FFMPEG.
WMV9 also seems to work fine using both the SDK and GUI tool.
I’m working through some Mac -> Venus issues with CS5 and saw this post. I’ll probably DM you through twitter as well, since I don’t spend a lot of time on the COW.