Mac OSX (10.6.6), Mail Version 4.4 (1082), and FlagIt! (1.6).
I marked an item as completed. Later on it wasn't, so I needed to re-flag it. Selecting any of the Flag-It flags does not change the Flag-It check. Clearing the flag removes it, but I cannot then add a Flag-It flag. If the check is cleared, and I select the Apple's flag option, then it simply turns the Flag-It check back on.