I had the same problem. On startup, iTunes (9.0.1) would repeatedly scan some (!) files created and imported with Audiobook Builder (1.1.2). On top of that, the meta data (Artist, Album, etc) of those files would not be editable in iTunes.
I tried fixing permissions in Finder and Terminal, to no avail.
I tried renaming the file endings from .m4b to .m4a in Finder. For one file that actually worked, and though I renamed it back to .m4b afterwards it could still be edited in iTunes. For most files this didn't work.
I finally got something to work that fixes the problem of files not being editable and files being scanned over and over again on iTunes start-up. It goes like this.
1) Locate the file created in Audiobook Builder either through "Show in Finder" in iTunes or directly from where it was saved.
2) Open the file in QuickTime Player (7.6.4).
3) Open menu "Window" -> "Show Movie Properties" (command-j) and edit the meta data fields you want to change.
4) Hit menu "File" -> "Save" (command-s) and enter a new file name. Don't mind the ending .mov for the file. The chapter markers, album cover, etc, are saved in the new file.
5) Quit QT.
6) Optionally rename the file ending back to .m4b.
7) Drag the new file into iTunes.
Enjoy!
I tested that the chapters are still intact when played in iTunes and on the iPhone. The meta data can now be edited in iTunes and the it won't be scanned again on start-up.
I hope this helps some of you!
- Manuel