I worked the greater part of the weekend color, gamma, etc. correcting a 13 min video shot by shot in Premiere and exported it to Motion JPEG B @ 100%. I then discover that I can't run this through mencoder/ffmpegX because it can't deal with the codec and instructs me to include it at "compilation" or something.

If ffmpegX is billed as being able to read .mov files, then it should be able to deal with any of the standard Apple codecs. If not, there should be a nice big list somewhere. MJPEG A does fine, but in this case if I export the B to the A in QT or even Premiere, it accentuates a slight shimmer effect, which will drive a codec crazy at final encode (Don't suggest using the denoise filter, which kills all the detail as well).

Is there any way to get mencoder to read MJPEG B?