I was playing a LAN game last night (after 1.01 patch), 2 humans vs 5 nightmare AIs on Zikurat. My ally and I took out the left towers all the way to their portal. We destroyed the 3 towers around their portal and capped the portal. Things were looking good as we both alternated porting back and forth between our citadel and their portal and flag locking. We also captured the left gold mine (protected by archer towers).
However, something odd happened. After a while, ALL their towers respawned (aside from the two very first ones that the grunts run towards after coming out of the neutral portal). This seemed to coincide with one of their war effort increases (can't remember which one). This was immensely frustrating as we had to redo all our work over again (although they did not respawn again after a second time, although we didn't destroy all the same towers the second time around).
This is the first time it's happened to me, but it seems like a pretty huge bug, especially if it was an online match.
For the record, they were not Rook towers, as they were permanent and spawned all at the same time.