Just found this. I went from 63 minutes to 44 with this edit.
http://sourceforge.net/forum/forum.php?thread_id=3295067&forum_id=884113
I've just been reading up on VideoMonkey and found that too. I'll try it all out when i get home. I have read though that even after that increase that the CPU still only uses 12% does that mean VideoMonkey is very slow at converting?
BTW did you see the comment below about setting the number to 0 so VideoMonkey can choose whats best (maximum)?