Are you sure that this is not due to what seems to be a re-indexing occurring as you add or delete a bookmark, or add highlighting?
I was plagued with this. Frequently, but not always, when adding a highlight, my k3 would appear to freeze, but if I waited long enough (90-120 secs, usually), it would return to life. If I got impatient and rebooted, the highlight or bookmark would have been saved. It also seems to be related to the size of your library. Mine is at 1200+ books.
Use debug and turn off indexing - details are in the forums somewhere. I did this in Feb, and have had no problem since then. BTW, this is not persistant. If you reboot your kindle, you will have to reset the no-indexing flag.
Snowman
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