You're describing normal preference through experience, not bias IMHO. So relax you're a really good person!
Seriously though, what you describe is unavoidable. We all develop preferences based on experience and what it signalled for us.
So, for example, if you play FPS on 360 and find the triggers great, then play the exact same FPS on PS3 and find the controller only okay, that experience colours your view. Your brain simply informs your emotional response (sorry, sounding very Blade Runner here) and you cannot avoid feeling the 360 experience was somewhat better. Conversely, perhaps with a fighting game or platforming game, the experience might reverse, with your brain recording the PS3 controller and experience as slightly better.
Sure, if you really concentrate and put effort in you can theoretically overcome just about any learnt bias, but that can be tough - because in the end you may be trying to compensate for something real - i.e. perhaps the 360 controller really is just better for you. I think you're denying your own preferences to go that far.
For my myself, although I can now enjoy an FPS on consoles, either 360 or PS3, because I first encountered FPS on PC, and still play FPS on PC, I always find the console FPS just that little bit lacking. If only this was on PC, I can't help musing. I guess I could 'force' myself to cancel out my knowledge and experience of FPS with K&M on PC, but why?
When your bias in uninformed, driven by immaturity, overly competitive behaviour and is unfounded then you need to worry.
Just enjoy what you play on 360 to the max afforded by your set-up, and ditto for the PS3 - oh, and try out K&M on PC for FPS, it's even better... whoops, letting my bias creep in there!
Try to be reasonable... its easier than you think...
