1. Seek tool data is stored on the dynamic data partition, the same place where playlists, running orders, etc. are stored. This drive is written to in raw mode, i.e. it's not really mounted at all. The player just writes to it using low-level routines. Don't know much more about it than that.
2. Screen burn is a legitimate concern on the empeg. The hijack kernel has a neat screen blanker which can help you out, but it also may blank the screen when you don't want it to.