Gil Finn
The Roundhouse Shay often needs tuning and work to run well. A loud noise may be an indication something isn't right, depending on what the cause is. Continued running when there is binding present may lead to more damage or parts not working properly. You need to figure out where the noise is coming from - motor, main gearbox, truck gearbox, universal joints, line shaft sliding joints, line shaft gears, etc, and whether or not any of these parts are binding.
Also, Shays were designed to run very slowly because of their low gearing. The prototype made incredible noise (most models do too) running above 15 MPH. Are you trying to run it too fast?
I strongly recommend "The MDC Shay Handbook" by Jeff Johnston - out of print but can be found used - as a guide for tuning the mechanism. A search of earlier threads should show some discussions of how to make this special model locomotive run better.
yours in gearing down