TSANTEE I don't know the answer to your question but Popcorn 3 now allows pausing encoding. This is from Popcorn 3 Getting Started Guide:
"Encoding can be paused at any time to free up the CPU for other tasks and then resumed later. When encoding is paused, you can run other applications or even switch to another user account as long as Popcorn remains open. If you close the Popcorn application, even when video encoding is paused, you must restart the process from the beginning."
I suggest raising your question on Roxio's Popcorn 3 forum.
(Version 3.0)