X-Perl had much of the same problems, but managed to cure it all this morning, so in the interest of fostering relations between mod authors; Here are some thoughts:
Basically got around the huge startup freeze by forcing the secure templates to startup after the first OnUpdate of a dummy frame which hides itself afterward. Had to move some things away from VARIABLES_LOADED to this new event. Very hard to nail down what the problem is exactly, but something about doing things too soon has become immensly slow.
Took a lot of trial and error with a good dose of frustration and hair pulling, and I'm not at all happy with how it's turned out. Feels very hacked atm, but it's working. With some more patience and time we can maybe identify the actual problem (or hey, Blizzard might fix it... hmm).
Zek, the problem is that this thing can still happen when you enter a battleground, not just when you login while in one.