I'm running Shimano LX M585 disc brakes and they're great. However, with the pistons fully retracted and pads installed (currently a new set of A2Zs) there's minimal clearance between pads and rotor, just a fraction of a mm each side I'd guess, I'd be lucky to be able to slip a piece of writing paper between pad and rotor. This makes aligning the caliper quite a job, but it's possible with just a little rub.
During riding though knocks and bumps tend to start the pads rubbing, although it usually stops after a while. Will the pads wear in after a while(they're properly bedded in)? The LXs are my first set of hydaulics (after using Avid mechanicals) so I'm no expert but I understand that the calipers automatically adjust for wear, if I sand down the pads slightly will the pistons simply 'adjust for wear' leaving the same amount of clearance?
It's not a major problem and the brakes work really well but I wouldn't mind reducing pad rub if I can.
The brakes normally have pretty decent clearance (up to 1mm each side), but many aftermarket pad manufacturers make the pad material thicker to increase pad life. It's a pain in the ass, but it will sort itself out pretty quickly. Nothing rubs forever!