Yes, the P2.89 software upgrade definitely increased the "lock" time for all OTA DTV channels. Those that suffer multi-path problems take a really long time, but when they lock, they seem to lock better and with a little higher signal reading.
My guess is that E* decided to tweak the discrimination capability of its software again. A software revision around summer of last year fixed the 49% problem that initial purchasers had w/ the unit. In that case, 49% stayed, no lock, for channels other STBs readily locked. So now they've pushed it too far the other way and the unit takes too much time trying to make sure it has the strongest, steadiest, signal before it locks.
They should have left well enough alone!