Why does the VPI motor thump

The only time I ever had a thump is when the motor cap went bad. I don't have the problem with a variac because there is no turn on / off of the motor, just the switch on the variac. I keep the variac set to 0volts for turn on / off.

You don't have any thump because you're using SDS.

I bought my Classic 2 used from a highly reputable store and then bought my Classic 3 at the VPI factory where Harry personally put the box in my hands. Both of these tables made the exact same noise when hitting the power switch. I have no personal problem with Harry as a person, he seems like a very nice guy but this particular issue is a problem. Customers shouldn't need to do a modification or upgrade to have a product work without problems. I don't think that this qualifies as "VPI bashing", I think its calling a spade a spade.

Have you discussed this with Harry?

Why not blame the preamp? Why not blame the AC cords or the ICs to the phono stage? If the stock cap works for 80% of the VPI tables, I would look long and hard at other components' placement and emi/rf sensitivity as well. Some components do not play well in proximity to some others. I have to be careful with placement of my phono stage and its separate PS to avoid problems like low-level AM radio and various hums reproduced through the speakers. Careful placement away from my amps and especially, the VPI SDS gets me superb sound while sloppy placement gets me mysteries to solve. Some placements I tried while getting to the current one also caused the turn-on thumping, but only when using the switch on the 2-motor/flywheel body rather than the SDS. This does not happen in my current configuration using all the same components and cables.

Solving the problem at the TT end might keep you from finding a solution that is also causing you not-yet-detected problems elsewhere in your system.