I tried many different things for running a dedicated amiga emulation "clone". After lots of trial and error I ended up using a copy of windows xp, stripped it down as bare bones as I could. Next, remove windows and replace with winuae/os3.9 as the shell.
You can also remove the windows boot screens and so on so you'll never even see windows (Unless you need to fix something) This is a very workable solution and works the best of everything I tried.
I tried for a long time to use the knoppix installation, but its buggy and under developed, and limited to 800x600 unless you mess with the xorg configuration files and so on, and even then its not very stable.
I think windows underneath but kind of stripped and removed is the best way to go, and I tried everything. Yes takes a bit longer to boot but once booted, its very stable and usable. I rarely need a reboot.
Who knew windows could be so stable. You just need to replace the windows shell with Amiga OS! hahaha
Steven