Well, this might be an easy fix. VerticalBlank used to look like this:

void VerticalBlank()
{
 InitSpriteShotDatastreams();
 DisplayShots();
 DisplaySprites();
 PrepScoreDatastream();
}

it now looks like this

void VerticalBlank()
{
 DisplayShots();
 DisplaySprites();
}

I built a special Stress Test ROM that starts out every wave with 12 asteroids. Initially I was seeing a few screen rolls at the start of each wave while destroying asteroids. Once enough had been shot the rolls stopped until the next wave began.

I moved moved InitSpriteShotDatastreams() and PrepScoreDatastream() into OverScan and haven't seen a screen roll or jitter since. It's not enough of a stress test to confirm this will take care of the problem though, for that I need a lot of playtime spent on this build. If anybody reports back that they experienced any screen rolls or jitter, then I'll review DisplayShots() and DisplaySprites() to see what I can do and make a new stress test build.

Note: you must play this on a real Atari using a Harmony cartridge in order to provide Stress Test feedback.

ROM

spacerocks20121001_STRESS_TEST.bin

Source

spacerocks20121001.zip