I spent a week with file vault 2 running but found the startup time of my 2012 Retina MBP was excessively slow (5+ mins on the grey apple screen after the spinning white thingo stops) along with the track pad becoming unresponsive for minutes at a time. I assumed/suspected it was file vault and turned it back off.
However the problem didn't go away so I erased the drive, installed a clean OS and it restarted perfectly. I then restored my full system from time machine and the problem came back (this probably shouldn't have been a surprise). I then erased and reinstalled again but this time used migration assistant to just restore home folder, applications and settings. The problem remains.
Does anyone have an idea that doesn't involve me manually reinstalling and rebuilding everything piece by piece? The thought of getting all my preferences back to how they are almost makes me want to put up with the problem.