[eluser]Phil Sturgeon[/eluser]
I have PMed you about this one. Might be an idea to keep support requests to a minimum and i'll either post bug-fixes to the repo or write up solutions in here.
I intend to set up dev.pyrocms.com soon anyhow so this will be officially working on sub-domains within a few days. Then I'll have a root installation (personal blog), a non-root installation (pyrocms demo) and a sub-domain installation (dev site). Then I wonder if sub-domain non-root will be an issue.... ahaha!