Just a quick suggestion is that many codecs (like quicktime mov container) don’t come as 64bit codecs. So they won’t be available in either Motion Builders rendering or video textures (input). You will probably have to stick with AVI format on the 64 bit version.
Motion Builder is a bit like a game engine underneath and certainly game engines (that i’ve used) don’t tend to support a lot of different video codecs - prefering to stick with a few and make sure those work solidly with the various means of playback.
There do seem to be lot of image formats supported by Motion Builder - think the bottom line is you want to use a format that doesn’t use inter-frame compression (compression which spans more than 1 frame to store any particular frame). Because it’s a problem for the software to quickly decode the thing when your, say, pausing on a particular frame or jogging slowly at a slow time speed.