If Premiere is acting weird.
Restart computer, hold down shift+alt while opening Premier.
Then trash all your media cache in the Preference (and manually) and preview files (under sequence)
See if that will help.
I just discovered that this problem happens when I have other stuff visible on Video 2 or Video 3 such as text or a still image, but only if visible, then if I render the sequence it creates the problem.
Anyway to fix it?