This is a not uncommon problem.
First, make sure the problem is not with the pins themselves. (It rarely is). Get a new set of SLOTTED bridge pins to test with, even if you plan to keep using the bridge pins that came with the guitar. (The plastic kind will set you back all of a buck or two for a full set.)
Test the new pins WITHOUT the strings in. If there's still a problem seating the pins evenly, then get yourself a tapered reamer. (Every guitarist should have one of these!):
http://cgi.ebay.com/ENKAY-720-C-TAPERED ... 0218294477
GENTLY enlarge the bridge pin holes that are too small, a quarter-turn at a time. Test the bridge pins to see if they reseat properly after each quarter turn. You want them to be snug in the holes, without the strings in, but to go all the way in. Generally, one or two turns of the reamer are sufficient.
Tapered reamers are also great for enlarging tuner holes in your headstock, because they enlarge from the center out, unlike with a drill bit.
DO NOT USE A DRILL, OR ANY OTHER POWER TOOL, TO ENLARGE BRIDGE PIN HOLES OR HEADSTOCK TUNER HOLES!
You can also sand the bridge pins, but if the problem is with the holes, it's better to solve the problem rather than dance around it.
Bridge pin holes can get tight for any number of reasons, but usually it has to do with moisture expanding the wood over time -- sweat, beer, or just what's in the air where you live.
The above should solve your problem, unless you upgraded to "boutique" bridge pins, some of which are not slotted. But from the pictures it doesn't appear that that's your problem.
Good luck!
Glenn Jones
Cambridge, MA