Squeeze just uses the same libraries for Real and WM encoding as the ones provided by Real and MS themselves, so there really should be no difference in what you can generate as compared to other encoding apps that do the same (like Canopus and Adobe). But, there may be a problem in the way Squeeze is handling the source color transition to the 4:2:0 color space of those codecs. Is there any way you can generate a YUY2, UYVY, or YV12 .AVI?