Ok, I found out some more weird behavior which may be related to what you are seeing....
I defined more than one portal, and I allowed personal portals.
I defined portal tables (simple html for now). I put portal tables in the portals I defined including the personal portal.
Whenever I update any portal, ACS 3.2.4 updates the portal ok, but at the same time it deletes the contents of the other portals! I can replicate this as often as I want.
This will definitely be in SDM.