I just ran into this On a lathe, but My noise problem got to were it was on all of the time..
I replaced the motor after doing the checks that you are doing now, and It didn't help.
Ended up being the servo amp. Why this causes a rumbling noise is beyond me. Mine would get worse the more heat it developed.
If your noise is mechanical in nature it won't go away unless something changes. I.e. it gets hot (which usually makes machanical problems worse) or something moved away from something else.
thanks
Michael T.
"If you don't stand for something, chances are, you'll fall for anything!"