This interests me too, I also run autoimport manually ... but I think I knwo what going on, Matt could you confirm.
To me "autoimport" does a bunch of things. OK it imports things, but it fixes things (reindexes them) - especially things done externally or via clients (play counts too), moving directories around, deleting things form the library. If syncing between client server is not run manually at the end of a client session, this happens all the time -- normal... for me as I have lastplayed written to file as an example.
I get about 6400 "analyzing" after import, which is about how many CDs (or maybe its the number of sub repertoires) with around 90K files -- this is actually pretty fast -- if it were actually importing all these files it is much slower.
In anycase, as long as you have Fix Broken links - protect un-connected drives checked, this is a good thing
@Matt - Is this about right ?