After some thinking about it, I think I see the problem.
If you did enable 'x264->Misc->Adjustments->Adjustments->Use internal decoder if possible' the problem is that x264 seemingly can't decode your file.
-> if this option is enabled ffmpeg or mencoder will be used to decode the file and x264 itself will not do the color conversion.
If ffmpeg/mencoder also fail and you can upload a small sample of such a file I can look into it and may be figure out a workaround.
If you got a vfw decoder installed for the Sony Packed YUV codec it might help to use the 'avisynth extension' this way AviSource should be used which than will use the vfw decoder. (not 100% so a sample might be good)
Cu Selur