FTE can mean a failure to EXTRACT or a failure to EJECT.... which was it?
I'm like Zanderman -- I don't understand how a magazine can affect or cause extraction problems UNLESS the upward pressure of extra-power mag springs are causing the top round in the mag to press against the underside of the slide, slowing it down. It would also be less noticeable as fewer rounds remain in the magazine. (If the 16-round mag springs are new/recently replaced, try them with a few less rounds to see if that helps. The springs will slowly take a set and degrade a bit.) Otherwise, a mag spring doesn't seem a likely cause for what you describe.
When other mags work well, it's logical to assume it's a mag issue -- but it could simply have been ammo issues. too.
I used to have a lot of problems with Winchester White Box... the design of the case, back then, didn't let the extractor get a good, consistent purchase on the case rim. I never noticed a problem with some magazines and not others, but I just avoided WWB like the plaguel Winchester seems to have fixed that problem and the case rim is different now. (I still avoid it.) Cheap ammo often gets fewer QC checks than the pricier stuff, so some variance in performance is possible.
Some years back, a bunch of CZ owners here on the forum found that going with a Wolff extra-strength extractor springs helped a lot, and CZ later upgraded that spring in the new guns. If you have an older CZ, a new extra-strength extractor spring might help.
I'll be interested in learning whether there is another (magazine-related) solution to this problem. I continue to learn new things.