Are they the 16 round or the 17/19 round magazines? I've never had an issue with the 16 round magazines but about half of the 19 round magazines will not fully insert into the mag well on my Pre B CZ 85. Something about the dimensions are just a little "fatter" on some of the 19 round versions.
I never thought about the back of the magazine making contact with the sear cage (anything is possible). If that's what is happening maybe the ejector is being pushed up against the groove in the bottom of the slide (seems like that would be a lot of "slop" though. If it was moving that much it seems like there would be detectable differences in trigger pull/feel.
You should be able to removed the slide/barrel and insert a problem magazine into the mag. well and then look to see if it's making contact with the sear cage. Wobble (or attempt to wobble) the sear cage up and down at the front, too, just to see if it's loose.
As for the slide not going quite forward when you slowly (hold it back, ride it forward, whatever it may be called) let the slide move forward, realize that won't happen when you are firing the pistol or releasing the slide from a magazine change. I have a couple CZ's like that. Easing the slide forward results in the slide stopping before it's fully forward/locked up. Here's a picture of my Tactical Sport with the slide stopped just short of where it needs to be. Just pushing on it with my thumb will move it forward - or letting it fly forward without babying it.