No, the gun was designed from day one to be as compatible with the barrel swap as possible. I'd be more inclined to think you've got a hinky barrel than a wonky extractor. Do you have access to someone else's P229 40? Ask if he'd let you put 100 rounds through it (installed in your gun, obviously). See if that works. If so, you need to replace your barrel.
First, I take responsibility because I'm the first one who brought the caliber "debate" into this thread.
Second, if we want to discuss the relative merits of 9mm vs. 40 vs. 357, let's begin a new and separate thread in the ammo & reloading section.
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