Don't worry, FileVault is perfectly stable and reliable and you really shouldn't experience any more issues ! I heavily rely on it myself (for testing and support purposes) and never encountered problems. :-)
Turning FileVault off and on again will force Mac OS X to create a new encrypted image, therefore solving any directory problems on it. However, for added security, I would recommend that you backup your data first and run a disk and permissions repair by using the Disk Utility between the two steps -- boot from the Mac OS X Install CD to repair the disk and from your hard drive to repair the permissions.
Also, you may want to make sure that you have plenty of empty space left on your hard drive : at least slightly more than the size of your unencrypted home.
Let me know if this helps !