Ran into two bugs: Compount Clips and In and Out Points

Just made a compound clip on part of a timeline so that I can rotate the whole thing and found that I kept getting issue with the audio breaking up almost like samples were being dropped and this would show up in the encode as well. Breaking it apart fixed the issue. Blur effects will also sometimes disable themselves when applied to compound clips. You need to go to the Edit tab, scrub over the area and then it will turn on again.

The other issue is the In and Out points in the Deliver tab. On some occasions pressing "Start Render" would cause the In and Out points to reset so that it renders the whole sequence. Stopping the render and setting them back to where you want them right afterwards will fix the issue so it won't fight you too much but I have had to do it multiple times already. I haven't found anything in particular that causes this to happen.