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Sorry to hear about your issue. I've spoken with ATI a few times and all of them, they've been very, very helpful. Exceedingly helpful actually. I would call them at 800-290-0065 to get your gun fixed,

Break in period may be ongoing. Ball ammo would function and power through small burrs. Recoil spring may be the problem if its not cycling properly. If mags aren't seating well, this can be very telling. Is the pistol well oiled (not over oiled or dry). I assume you may know also this since you polished your slide and its a nice pistol. I'm guessing you're no rookie. Extractor tension may need tweaked too.

Getting a 9mm 1911 Commander size with a bushing and non-ramped barrel can be problematic. Most run well in the cartridge they were designed for which is 45 ACP. I'd check the bolt face to see if the head of the cartridge can easily slide up it. Sometimes there is a burr around the firing pin hole that needs to be removed. Does it run with less than 9 cartridges in the magazines? The cartridges tend to nose down once you get more than 8 of them stacked. Do you have the old Wilson magazines (plastic followers) or the new ones with the steel followers? The ones with the steel followers run in everything I have but the plastic followers were a problem.

If it is still in warranty send it back to ATI here is the number for them 800-290-0065, also came across this info but from the the looks of it you already tried most of the things they were talking about https://forums.1911forum.com/showthread.php?t=356239