I'm having this exact issue as well (plus another one on the B-board, but that's another story).
On SSF2 I have the sprites (fighters and health bars) flickering, everything else is ok (background, music, etc.).
Where do I start looking? The motherboard looks immaculate, can't find a single sign of corrosion.
EDIT: some additional info, thing I've already tried to do:
1 - Remove all socketed chips, cleaned connectors, reseated all the chips.
2 - Clean the boards (both A and B)
3 - Made sure there's optimal contact between the two boards
4 - Checked all the electrolytic capacitors
5 - Looked carefully for any sign of corrosion or broken traces
6 - Inspected the connectors, looking for broken/bent pins
I've heard that the 74LS245 are prone to failure, but how do I tell which has gone bad?
EDIT 2:
So, I've tried reflowing the connectors since I've read that those points are prone to crack, nothing changed so far.
One thing I've noticed is that "INSERT COIN." is written not in all caps like it should, it uses all lowercase letters.
And one more thing: I tried going into the test menu to scroll all the graphic tiles and the only one flickering are the Object ones. Everything else is fine.