Yes, the feedback resistors were changed from the first batch, but I don't think it is unrelated to bias issues. I had an early pair as well and didn't have any problems with bias. Parasound solved a few glitches in early units and reports excellent reliability in more recent production runs. I hope you're aware the ten years parts, five years labor warranty is valid only to the original purchaser and when purchased from an authorized Parasound Halo dealer This policy is pretty common in the industry - it is always advisable to call the manufacturer to ask, if considering purchasing used or from a non authorized seller.
You are correct, merely leaving the amps turned on isn't enough to break them in, you need to be running signal through them at all times. Knowing that, go ahead and break them in and see if you don't notice some dramatic improvements at around 1200 and 1400 hours. I agree with others suggesting there should be no lack of bass in your system when set up optimally.