Seriously. Gotta make sure you bleed that system properly. My friend and I did it when I upgraded my fronts to 13" rotors and the corresponding calipers. Any time you have the brake lines open to the air, gotta bleed 'em afterwards. Changing pads, not so much, but if the calipers are off...most definitely.
When one bleeds brakes manually, it generally goes something like this:
1 start at wheel furthest from master cylinder
2 person at wheel installs clear plastic tube on bleeder screw and runs it down into jar with fresh brake fluid in it; end is submerged
3 friend in car pumps brake pedal once or twice and then holds it
4 person at wheel being bled opens screw a bit and observes bubbles leaving caliper in tube as fluid moves into jar
5 person at wheel closes bleeder screw before pedal hits floor
6 go to step 3 and repeat until no bubbles are observed leaving caliper
7 verify fluid level in master cylinder and re-fill as necessary
8 if last wheel, go to step 9 else move to next furthest wheel and go to step 2
9 have a beer
When you were bleeding, did you actually see fluid leaving the calipers and did you only move to the next wheel once no air bubbles were seen leaving the caliper?
Did the master cylinder run dry?
If you just removed calipers air shouldn't have moved all the way up the master cylinder...