WordPress 1.5 overwriting Frontpage extensions

I tried using permalinks for my blog at http://christiansontheclock.org (not trying to spam url – just if you need to look. It worked, but must have overwritten my frontpage extensions for another site that is a subdomain of that one. Reinstalled FP extensions, but the permalinks crapped out & my feed dissappeared.

Anyone know how to keep this battle from occurring?