ML Sleeps While Programs are Running

Twice now, my iMac running Mountain Lion has fallen asleep while a program is actively running.  (Ex. Encoding a movie in Handbrake and burning a BD disc with Toast.)  Does anyone know why this is happening?  I have never had issues with my Mac sleeping during such processes before. I actually count on this because I very often walk away as these longer processin tasks run and/or start them when I toddle off to bed.  I hope this is something I can resolve and not a bug.

According to Ars Technica:
"In Mountain Lion, OS X no longer pays attention to disk activity when deciding if it's OK to put the system to sleep. Instead, Apple recommends that applications make what Apple calls "power assertions" as a way to tell the OS when they're doing some useful work that the system should stay awake for. This policy allows the OS to put the system to sleep the moment there are no applications still holding power assertions to prevent the action."
Apparently the "caffeinate" terminal command can be used in conjunction with specific processs to keep your machine awake until the process completes but it also seems that apps will have to be updated to comply with this new power management protocol. I've noticed the problem with Retrospect 9, HandBrake and RipIt so far...
I have not figured out the terminal commands for using caffeinate with these apps—if anyone has some pointers I would be grateful.
Thx

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