First thing...good on you for using the front brake so much. So many people out on the trail sliding the back wheel around...bleh!
It's normal for a lower line bike to have inconsistant pad retraction, lower tolerances in hub axles and bearings, and other random things that drive me crazy. Even mid-level brakes like Avid hydraulics will occasionally have this issue of inconsistancy. My elixirs are doing fine though.
Best thing to do is loosen the caliper bolts just enough that the caliper will move laterally...clamp down on your front brake...hold tension...tighten the caliper bolts. This should center the caliper.
There are occasions that this doesn't work...in these cases, you can either use a couple of shims (one on either side of the rotor between the pads and rotor)...or you can just eyeball it to center.
If you find this happening on a regular basis, it would help to localize the issue. If you're running mechanicals, it's not an inconsistancy in pad retraction b/c only one side moves. If you're running hydraulics...it could possibly be inconsistant piston retraction. Just look at it really closely when you let off the brake.
If you find that it's not the piston...then you need to decide whether or not it's worth it to upgrade to a more expensive front hub. You can find some pretty decent front wheels laced to an XT hub for a fair price on eBay, bicyclewheelwarehouse, and other online vendors.
Make sure your front skewer is tight enough btw, LOL.