The following issue applies at least to Ubuntu 12.04, and does NOT apply to Ubuntu 10.04.
It took me about 30 minutes of trying to find an error in "Flyspray", while the problem was somewhere totally else:
Then I found that in
/etc/apache2/conf.d, a softlink exists to the file
Not sure what exactly Virtualmin can do about this... Maybe disable that intelligent .conf up there upon installation. :) Not classifying this as a bug of course, since it's not VM's fault.
I guess I'll be staying with 10.04 for my production VMs for quite a while. :D The disastrous security flaw in MySQL a while back, and now this, do not really improve my confidence in this new version.