Keep in mind that we don't have official support for The G.E.C.K. -- this is no different than Oblivion or Morrowind. As such, we're not testing new updates against existing mods or accounting for backwards compatibility for mods. Still after the PMs I received, I wanted to pass along your feedback.
In other news, there is a new update to the GECK available. See details http://www.gamesas.com/bgsforums/index.php?showtopic=985995.
GECK update! Pwnage!! Yay!
So yeah - - the thing that gets my attention about this issue with 1.5 and persistant refs is this - - - -
The DLC ya'll developed does not use .esp files. They are all based upon .esm.
The patch made a change to how .esp files are being handled by the .exe. It doesn't cause mod conflicts, it causes the game to use .esp files in a new way, and that new way doesn't parallel the way the .exe is handling .esms. And the end result is that mods made in .esp format have problems.
The way those things work together, combined with the fact that it makes .esp files much more limited in practical usability than before, gives me the hunch that it was an unintended side-effect of something that was done elsewhere. And it wouldn't have been caught by QA because that test environment wouldn't naturally include .esps in the load order.