Hi, I'm not sure what else to suggest but you could try opening the options file and changing:
'VertexBufferMethod=1' to 'VertexBufferMethod=2', or trying the 'AlternateSyncMethod'.
I've also heard mouse/controller drivers can cause problems like this so I'd suggest seeing if unplugging / changing ports has any effect.
Finally I'd suggest googling the same problem for games like Nuclear Throne and Undertale because they use the same engine and those games are much better documented than mine.