Flushing your brake system is fairly simple...
1) Locate the bleed valve on the caliper assembly
(the valve looks similar to a grease zerk). Find a piece of tubing to attach to the bleed valve to drain into an empty container (I use 1/4" clear fuel tubing).
2) Pump you brake level several times, then, hold the lever in a slightly depressed position. Now while holding the brake lever steady, open the bleed valve approx 1/2 turn with an open end wrench until fluid starts to come out of the valve.
3) Slowly depress you brake lever to full compression. While holding the brake lever there, tighten the bleed valve back to it's original position. DO NOT RELEASE THE BRAKE LEVER WHILE THE BLEED VALVE IS OPEN!
4) Once the bleed valve is tightened, release the brake lever. Now go back to step 2 and repeat.
5) Monitor the level of brake fluid in the resevour. You will see it begin to go down. Continue to above procedure until it is "nearly" empty (do not completely empty the resevour!). Now, fill the resevour back up to the fill line with new fresh fluid.
6) Now repeat steps 2-5 again until the fluid coming out of the bleed valve is clean. I usually have to refill the resevour 3-4 times before the old fluid is completely flushed out.
This may or may not fix your problem, but would be a good place to start. This is also a good procedure to learn as the brake fluid should be changed annually anyway.