If the issue(s) you're experiencing are the same as described in
this forum post, the evidence we have indicates files of 2.5 hours in length or less are much less prone to stopping/skipping ahead.
It can be tricky to end up with files of that length because Audiobook Builder's current method of segmenting its output into Parts doesn't treat your preferred maximum Part length as a hard limit. It includes all of the audio from the last file to be included in each Part so that it preserves the original pauses inserted by the artist or production team. If it didn't, each Part would very likely end mid-word, mid-sentence. The way Audiobook Builder compensates will almost always result in Parts that are several seconds to several minutes longer than your preferred maximum Part length.
While we haven't received a final word from Apple on the cause(s) of unreliable playback on the iPod I would lean away from file length as the only underlying cause because the issue has not manifested in any of our tests when the audio files are not set up as bookmarkable. That leads us to maintain the issue is very much related to the way the iPod handles bookmarks, and file length is somehow involved. Would that we were within Apple and could buck the system to get some real information into the hands that feed them...