What exactly is the "lens glare" problem? I'm at the end (nothing to do but Ganondorf's castle) and I've noticed no problems with the lens of truth. I use the default install package (no changes to plugins).
All cutscenes so far have been flawless. The only problems I have is silver being redered as grey, the glow from opening special large chests being translucent black shadows instead of gold, and heart containers showing up as transparent pink (not red).