I’m having the same trouble w/ CS6 and reading reports of this from back in ’08 – which makes this issue going on 4 years old now.
Same deal: random* keyframes become unmoveable in the timeline. They are selectable only by drag-over selection, but still not moveable.
Anybody hear of any fixes or clever workarounds? Tried the drag/select/copy/paste but no dice. Turned off live update, multiprocessing, and no help. I’ve only got about 40 layers. *In my case it seems specific to time remapping keyframes.