Great! I would re-run Audyssey since you have been fiddling with the sub controls, and especially because you defeated the crossover. The electronic filter in the sub introduces some delay which causes Audyssey to compensate; a big element of Audyssey's calibration is the TIME alignment of your system.
So, once you have the sub controls tweaked to your liking (volume is solid, low-pass is defeated, phase at 0, etc) re-run Audyssey. You will probably have to re-tweak any changes to made e.g. to crossover frequency in the receiver.
In general, once you run Audyssey you shouldn't touch the controls on the sub, and instead do everything digitally in the receiver. If make any physical changes to the system (either repositioning the sub or playing with the dials) you should re-run Audyssey so the system is still calibrated.
Enjoy And all you other 1610/590 owners, please keep some reviews coming.