To be fair, the OP was discussing both a Tormach computer system and another system with similar issues. I don't own a Tormach machine, but do use the tool holders. Just ordered another today.
What I take from this thread is that you have to do your due diligence in order to trouble shoot issues that may arise, whether it is a safety, economic or just a pesky situation. Don't just blame Mach 3 for the issues. You may wind up there, but at least then you will know where to research a remedy.
On my router for a time with the R40 laptop, my router would start bumping on and off during start up of the computer. It runs under Mach control but only after Mach 3 takes over. Not while the computer is booting. Now this is where a charge pump would really help if the BOB is so equipped. Mine wasn't, so I started trouble shooting.

Everything in the control panel was running on the same surge protector including the router. The fix, short of a new BOB, was simply to plug the router into a different circuit nearby. This has fixed that issue, so it was apparently a noise issue. I will say that I do plan on the new BOB though. I am planning on the complete control cabinet rebuild that will take it from the original hobby setup to a pro level control cabinet.

Tormach obviously gets these computers designed for them or at least tests them before including in a package. Same with Novakon.
For anyone with any computer running cnc or not, I will recommend using an SSD. I have upgraded my desktop and my Torus came with one already, but boots are maybe 30 seconds. A bit faster on the Torus, because it only has Mach 3 installed.