Thank you for responding!
I was watching the produced video when I first noticed the discrepancy. That's when I started trying to dig.
I'm assuming the issue is related to me using the same 4 video clips over and over again, trimming down to only what I need. I wouldn't have expected it to cause any issues. I'm 90% sure all the clips are the same type - recorded footage from a Hauppauge HD PVR2. Maybe the intro clip I'm using is set to a different frame rate or something.
My PC is a beast - i7 4771 3.5 Ghz quad core Haswell with 32 GB RAM on Win 7 Ultimate 64-bit.
I'll verify that all clips are the same type. Apart from that, I'm considering actual making 15 small video files and just dropping them in.
Thanks!