The first, and most important one is that there's no sound.
The Linux versions I provide don't have sound enabled because of the difficulty of making it work across many Linux distributions.
You can compile your own version using the '-sound 1' option. See the Build system documentation.
However the version you compile on a modern Ubuntu distribution probably would run not on most other distributions. The version I provide is compiled on a very old version of Linux, and does happen to work on most distributions, except for the sound issue. Lately I think I see a way to make this work better (basically copy how SDL does it), which I hope to get around to trying some day.
I'm not a Linux expert. Linux is a pain to support since systems are so diverse, and each of the many versions can have their own quirks and bugs. Mac and Windows system versions also have their own quirks and bugs, but there are far fewer versions to worry about.
The second one is that the Mini vMac's window has the desktop picture showing through on the right and bottom.
Ugh, case in point. I'll have to download Ubuntu 9.10 and take a look. There is likely a bug in it, since I've never seen this behavior before. Though it's also perfectly possible that there is some obscure bug in Mini vMac that doesn't manifest anywhere else. Anyway, thanks for the bug report.