Encrypted system bugs
A PDF version of my encryption guides (with referenced links for convinience etc), which you may find much easier to read is available here.
Overview
Since writing my encryption guide a few bugs have come up, check here to see if I've come across the one you are having problems with.
Resume from disk and Compiz or Compiz Fusion
If using Compiz you may find when resuming from disk that you get a cursor, but no desktop or keyboard input. To fix this disable 'Sync to Vblank' in CCSM (or whatever Compiz config manager you use).