What hardware was this running on?
FPGA machine by any chance? The only times I’ve seen issues like that are on FPGA machines with less than perfect emulation. In some cases updating them to the latest core can fix it.
I've just tried to reproduce this with 4.9.1 (also 4.10.0) of WinUAE (both 32 and 64bit versions). I ran the floppy version as it looks like that was what you were using. I tried PAL and NTSC versions. I tried official ROMs and AROS ROMs. I can't get the problem to occur. Almost all testing was done using WinUAE, and I probably played it a thousand times so something odd is going on here.
If you can get it to happen repeatedly, it would be useful to have your WinUAE config file, or you may have been extremely unlucky and hit a very rare problem. You could also try moving to WinUAE 4.10.1 which was just released.