Just had exactly the same thing happen on the Horde side. Used the new portal from event-Icecrown to go to Org, was flagged on arrival and appeared to be in the war mode version of Org as there were a few scourge and some dead folks on the AH steps. The timer expired, but I remained flagged. I tried flagging myself and switching it off, but it didn’t cause the flag to expire. Switched to war mode–which did not appear to change my phase at all–and switched it back off, but remained flagged with 0:00 remaining. Taking the portal to Dazar’alor allowed the timer to expire properly and unflag me, so hopefully you’ll have some luck waiting it out in Boralus.
Extra info: I noticed that it was nearly time for Bronjahm, so I took the Dazar’alor portal to Org, which did not flag me, and then took the portal to Wrath Dalaran which did flag me. (The existing portal to Wrath Dalaran. I didn’t notice the new portal near the command board earlier.) The flag expired properly at the five minute mark, though. For experiment confirmation reasons, I went back to Org via the new Icecrown portal and was again flagged, as is everyone else I see in town.
Maybe it’s intentional, so phase two of the pre-patch event gives us more scourge interaction that we can otherwise get away from by leaving the area if we don’t want it?
Edit: Argh. I just noticed this thread was actually raised from the dead, and the OP posted nearly two years ago.