September 4, 2009 7:30 AM PDT
I agree with all the above. I would definitely find what the problem is and FIX it. There are two things on my motorcycle I never put off if I think there is even the slightest problem - brakes & tires. Problems with either of these could KILL you, anything else will just cause an inconvenience.
I would pull the pads off the bike (pretty easy on the Fat Boy) and check to make sure there is no damage or something embedded in one of the pads. Hell for the price of pads, you should just change them while you have them off, unless they are really new and absolutely no damage.
Inspect the discs for scratches, dings or any other damege. Check and make sure they are not warped. You can do this buy getting the tire off the ground and spinning it slowely while watching the disc from the rear, straight on. If the disc is warped, or damaged, get it turned or get a new one.
And as Rex said...I hope you fixed the problem with the fluid being empty. Brake fluid does not evaporate. If it was empty, there was a PROBLEM.
Let us know what you find, and if you have any other questions, just ask.