The Air doesn't wake up from sleep mode when the lid is closed. Have to do a hard restart by pressing the power button for 5 secs which isn't nice. Tried to select the startup disk from system preferences but it isn't helping. This behavior seems to have started after I started using the PGP disk encryption but I am not sure if anyone else has experienced the same problem.
If you have TinkerTool System installed, waking when the lid is opened is a setting that can be turned off. Whether or not you have it installed, I'd suggest getting it and using it to see if it's somehow been changed. (Not sure how this might happen, but it's certainly worth a shot.)
TinkerTool System Release 2 > Mobile Settings > Wake Up, if you're wondering.