'Paste' to add sequence to alignment initially repaints incorrectly

Noticed in JalviewJS (where repaints are handled a bit differently) but can be reproduced in Java:
1) suppress call to paintAlignment in ConsensusThread.run() and ConservationThread.run()
2) load uniref50.fa, hide annotations, reasonably tall window (spare height)
3) select second sequence (FER_CAPAN) and Cmd-C, Cmd-V to copy and add to the alignment
Alignment is not drawn correctly - see screenshot attached.