FreeBSD Problem: Can't see files/dirty state at each boot.

Weird problem. The filesystem is in an unclean state at each boot, even though I have ran fsck before booting the system. Initially, our problem is that our app can't "see" certain files at first read, although subsequent attempts on reading them are OK. Later, we discovered that the filesystem is dirty at each boot. The problem is similar to this issue in FreeBSD-CURRENT. We're using FreeBSD 7.0-RELEASE though, so I'm not sure if we have the same problem. I need to track this down.