Hi,
I use Mcdsp's FilterBank plugins as AU in Logic, and discovered recently during a mix that there was something funny going on with the polarity. I then just used a different plugin and moved on, but today I had time to test it properly; recorded a bit of a sine wave, made a copy properly aligned to a second track, inserted a FB plug on both tracks, bypassed the other... and the audio files cancelled. I tested with and without delay compensation and also with other plugs to make sure it was not a Logic thing.
FilterBank v.5.0.6 and 5.0.8, Logic Pro 9.1.3
Haven't tested the ProTools versions.
R.