After upgrading to Mountain Lion this weekend I started noticing that active programs I have running like Handbrake seem to go into hibernation when the computer sleeps. Instead of completing the conversion over the course of the night as it usually does, I'm finding it still active and running when I wake the computer in the morning (presumably it isn't running all night long, but starting up again when I wake the machine). Anyone else run into this? Happened last night when I was running Pavtube Bluray Ripper as well. Came home after work and found the movie only ~40% done after starting it nearly 18 hours before hand. Note: this is happening on a current gen iMac 21" 2.5 i5.