I'm not too sure i got the question right but: Have you tried to clean the polarizers? If they're dirty it not only shows dirt, it also interferes a bit with polarization (slight ghosting increase). Otherwise it can only be the filters that aren't identical (either glasses or the filters).
The things that happens if you burn a polarizer (yes, i've done it.
) is that they don't physically burn. They just stops polarizing the light. At the beginning i used simple camerapolarizers for my rig but they soon checked out.
Align the filters as far away from the lense as possible but at the same time keeping the beam within the filter. Having bigger filters will help. I had 2500 lumen from the projectors and fried the filters but i think having a distance of maybe 7-10 cm's from the beamerlens could make a great difference (i had 0.5 cm's from the lenses).
Mb: Asus P5W DH Deluxe
Cpu: C2D E6600
Gb: Nvidia 7900GT + 8800GTX
3D:100" passive projector polarized setup + 22" IZ3D