The first thing that I would do is use an inexpensive USB microscope to see if there is any build up, or glazing, on the stylus that resists cleaning with conventional methods. If it is there, you can usually send it to one of the retippers for a cleaning at very nominal cost.
A bit more information, please. Who did the alignment, and has the tracking force been verified using a second guage? What tonearm are you using? Is this a problem on every record played, or only a sub set? When you say you clean the stylus after every side, is that with a brush, gel, Magic Eraser, or other means? And, most of all, good luck in finding a resolution to the problem.