The problem is when I browse the directory using MC 10.0.161 2 of the files won't show up. These files will play in iTunes though. They are each around 150mb, but there is a bigger file that does show up. What is wrong?
From your description I guess that you have encoded them directly to *.m4b with FAAC, right? Since MC is using QuickTime for decoding MP4 files (obviously including the *.m4b file extension) and had problems recognizing some tags because not scanning the whole file (now assumed to be fixed), your problem might be caused by the MP4 header infos being placed somewhere else than at the beginning in your huge files. This is allowed in the MPEG-4 standard, but not all applications "know" this.
Anyhow, to solve the problem you might try to optimize the MP4 file layout with external tools like mp4creator (command line) or foobar2000 with foo_mpeg4u.dll where you could choose this option in the context menu of a MP4 file. But you would have to change the file extension back to *.m4a or *.mp4 first, because foobar2000 doesn't know *.m4b files yet. Optimizing a big MP4 file takes a while, because it's rewritten in order to place the header infos at the beginning.
By the way, are your *.m4b files tagged? And how did you encode them, i.e. on the command line or with some GUI tools? Which FAAC settings did you use?