I've just had a slightly odd experience with AllPCB.
I ordered some boards from them a few weeks ago as a test, and they came back spot on.
Then, a couple of days ago, I put in an order for another design, and it got queried. No NC drill layer, apparently.
So, I checked the ZIP file I'd uploaded, and it's definitely there, so I emailed back to point this out.
AllPCB came back with another request for the NC drill layer, so I re-generated the file exactly as before but with "ncdrill" in the file name, replacing the original file in the ZIP.
I sent the new ZIP and my board is now, apparently, being fabricated. Hurrah!
I wonder if there's a language barrier problem? Maybe their front end software looks for files with "nc" or "drill" in the filename, and can't find the drill file otherwise?