Sorry, I forgot the details. It's a MK2a running 2.0 Beta 11.
I just deleted a few tracks, with 11547 entries when shuffling the entire contents and it was remembered across power cycles. I must be right on the border of some limit. I've actually had over 12000 tracks on the unit and the playlist was recalled across power cycles. That was before I did a lot of cross-referencing though.
I'm just wondering how the limit is determined, as I still have a bit of cross-referencing that I need to do and I seem to have bumped up against a wall.