1) It randomly marks tracks for some reason.

I've seen this before, but I'm not sure whether I'm remembering it from an internal release that definitely did have this problem (a piece of code deliberately marked the tracks if they were a different duration than claimed in the *1 file). It's alleged that it was disabled for the alpha.

I'll try resetting all of the marked tracks, and I'll see if any of them get re-marked.

2) Play counts seem to be often incorrect (some tracks I'm sure I've listened to still show 0 plays)

Can't say I've been paying much attention. Play counts seem to be working reliably for me.

3) Bookmarks are very unreliable (about as reliable as playlist saving)

I don't use bookmarks, so I can't comment on this one.

I've got a playlist of 5585 tracks loaded at the moment, and it's been working fine -- I've taken the player in and out of the car several times.