Definitely a cleaning and waxing will make the flippers feel stronger because the ball will fly around faster. I find a freshly waxed game more fun because the ball gets so wild.
The mechs are going to be identical between a first run and a later run game. It's most likely something mechanical, like the flippers being 1mm too high or low and having too much play or drag. Move the flipper with your hands and compare your games. Does the MMR feel different?
I recently replaced some flippers on a game and thought I had done a fine job but later realized there was major drag on the right flipper and had to re-do it.
Also it's possible the additional 1500 plays have added enough coil dust to the sleeves to make a noticeable difference.