I've managed to reproduce this with ADFFS 2.74, but only when run from the WIMP. It might be an issue with <Populous$Dir>.Title as I can't reproduce it if I comment it out in the boot script.
Shutting down the JIT and restarting it between the <Populous$Dir>.Title and Run <Populous$Dir>.Loader lines also appears to fix it. I'll continue investigating, but this issue does appear to be specific to this game and not related to 2.80
I have however noticed that CTRL-ESC when in the game crashes under 2.80, so I'll need to investigate and resolve that.