It's kind of tough to diagnose your problem without seeing the gun. It could just be weak ammo and after a few hundred rounds, it might break in nicely and work just fine with a 9mm buffer.
On the other hand though, WWB is usually pretty decent ammo and not underpowered - it should cycle the gun just fine with a 9mm buffer, even a brand new gun during break in. It wouldn't hurt to re-check the lower and also check the upper and make sure the ejector and feed ramp aren't dragging the bolt and the action cycles somewhat smoothly (nothing binding in the buffer tube - the action spring is sometimes a tight fit on the 9mm buffer so check that).
As far as risk to your receiver running a light buffer? Who really knows? Technically, every time you handle or shoot it, there is some element of risk that a part could break. In reality though, how much sooner would/could it fail? I don't know that anyone has tried both ways and can say conclusively that one way will fail X number of rounds sooner/later than the other. I have not seen a buffer tube fail in person. Come to think of it, I'm not sure I've even seen a pic online of that either.
As far as your theory on the round in the mag knocking the case off during extraction, I have seen that with some mags, but not with Metalform mags. If your fired case is falling off prematurely during extraction, you may want to check your extractor tension and possibly clean the extractor tunnel in the bolt.
When you say you are using a de-milled parts kit, are you talking from a lightly used demo gun, or from a heavily used training gun?