Hi,
I encountered this bug while using the Diplomacy mod; however, I am not sure if the Native doesn't have it. I already made a topic about it in tech support forum (http://forums.taleworlds.com/index.php/topic,158139.0.html), so I'll just copy&paste my report here:
I successfully completed the rebellion for Swads. However, some characters are left in the Swadian Rebels faction and are nowhere to be found.
Since it seems that this problem has not been reported yet, I'd like to elaborate further. First of all, King Harlaus was imprisoned by me and still kept in the dungeon when the rebellion succeeded. At that point some of the lords' behaviour seemed pretty glitchy (they threatened me and when I asked them about a location of a character, the list included King Harlaus at the top). Then I released the king, so he 'left' the game and the lords started to act normally once again.
However, some women are still listed in the 'Characters' list as being in the Swadian Rebels faction (and being Lady of Suno's vassals), though no such faction is listed in the 'Factions' list.
I think that this problem can be fixed with a small script, triggered by a dialogue with a chamberlain (for example). It should loop through all the characters in Swadian rebels faction and move them to the plain Swadian faction and also place them in the village in which I triggered the script. Unfortunately, I have no knowledge of M&B's scripting, so any help would be very, very appreciated! I fear our newly established realm might suffer from the crippling deficit of brides (it seems that almost all unmarried women are still in the rebel faction).
UPD: Also, my allies never join me in battles anymore.