Sometimes the reel basket (wheel the strips are mounted to) is a little loose on the stepper motor spindle. If you move the reel gently by hand does it have some looseness? On reel#2 do all of the strip symbols line up slightly low, or do some align properly and others do not? If all of the symbols on that reel align slightly low then you can try reinstalling the strip onto the reel with a little offset to correct the problem, or move the optic clip on the reel (if yours has one). For example, the reels on a WMS machine have an optic clip that you can move to make the symbols align better with the payline, but I don't know if your machine has this optic clip.
Also, in the casino the strips often do not align perfectly with the payline and sometimes at home we get a little too observant trying to make it exactly right. The average player wouldn't normally notice this. It's like putting up wallpaper, you will see all the little things that are not right but no one else will notice.
You can try switching the reel#1 with reel#2 to see what happens, that way you can narrow down what is causing it. But keep in mind that the basket is made of plastic and the strips are wrapped around it, so it isn't a precise thing.