Sounds like you might have some mags with slightly mis-cut mag latch holes, ie too low relative to the actual latch location. See if you can measure accurately from the front top lip of the mag, to the top of the latch hole on both mags. They should be the same. If the 8 rounder's holes are lower you may need to file the top of the hole a little bit at a time to fine up the fit. Or if out of spec bad enough, send them back to Kahr BEFORE you grind on them.
ETA: I see where you said the stripped mag "shells" latched in with no problems. If you will measure the heighth of the black polymer baseplate and email/IM it to me I will compare it to mine to see if there is a dimensional difference. Thats the only other thing I can think of that might be interfering with mag seating.
I have four of the 8 round mags for my CM9 that have worked flawlessly since day one. No problems loading the mags, or inserting them, loaded, into the gun. I use a Mag-Lula pistol mag loader so loading rounds into them is very easy and fast. Kahr mags are "almost" universally interchangeable within a given caliber and given model series. C series mags fit most all C series guns, T series mags in T series guns etc. Some of the 6 round mags might not work in some mid and full frame size guns, but all of the 7-8 round mags will work in all same series guns.
http://www.kahr.com/kahr-mag-guide.asp.
The link above will help.
And as an aside, I discovered that my standard 1911, ten round 45 acp magazines work in my CM 45. They run great, but they don't hold the bolt open on the last round. Nice to know in an emergency