Applying Convolution (In 2D) Theorem Swaps Quadrants
It's probably due to how you padded the filter before DFT'ing it.  I bet you had it in a corner instead of in the middle.  Since convolution via DFT is circular convolution, it's not so much of a quadrant swap as it is a wrap around.  I believe that if you put the non-zero taps in the middle that it will fix the problem.