This is my first time using Roxio support website in the 3+ years I've been using Popcorn, and just to say:
I'm having exactly the same problem (still using version 2, but problem is IDENTICAL). I would pay to upgrade to 3 if it fixed the problem, but it appears that it doesn't. I hope Roxio is reading this thread and working on a free fix for version 3 users!
Otherwise I'll not offer any more of my cash.
Thanks for posting, everyone, I learned a lot here.