Working with my host to find out why my permalinks keep disappearing it turns out that altering the W3TC configuration is the culprit and results in one or more of the .htaccess files being deleted and rewritten with only the W3TC stuff in them, no WordPress permalink rewriting and everything else you might have added is gone. Now it could be a configuration issue on the server, maybe an ownership or permissions kinda thing, but this behaviour is odd. I have never see it before and really should not happen of course. Any ideas what to check to see if its causing it? I am running the latest development version of W3TC now (WP 3.2.1. + W3TC 0.9.2.5b), but that does it too.