First off, sorry to hear about your problems with your amp. I can relate...I bought my Ace new and had intermittent grief for over a year before it could be fixed.
Next, pardon me if I missed this but I do not recall if you had actually tried to replace any tubes. If the shop saw no issue, they would not have either. This is a common cause of trouble and I can't help but feel Mesa would/should have you try this first.
If it were me, I would get at least 2 spares of preamp tubes (more than one can be bad and it never hurts to have extra spares....you WILL need them one day). You should also get spare output tubes as well (el84...come in pairs...Mesa only while under warranty, to avoid problems). These tubes do all the heavy work and will wear out regularly, now and then. That's normal and you will use them eventually...no wasted $ there. either.
Start with the output tubes, go to practice and see if it happens.
Also if it happens ONLY when you use 5 watt mode, which uses just one tube, swap them in the sockets and see if you still have problem.
Actually you can try this before you buy any new tubes...that may save some money.
Next, if trouble still happens, try the small preamp tubes (12ax7) and replace one at a time. If this does not happen in all modes, channels and settings, you can eliminate certain mode-dedicated tubes (the manual tells you which does what).
If the tubes are the issue, Mesa will exchange for new ones (well, if still under warranty).
If you are uncomfortable doing any of this, go ahead and take it in....but Mesa does encourage us to replace tubes first.
If not a tube issue, could be many things. My Ace had a bad filter cap in the power supply and would do similar to what you described except it would also act up when switching out of 'standby' into playing mode. You did not say you noticed this.
A bad cap will definately drop out the sound.
Hope it gets repaired quickly either way.
It could be worse. It took 2 months to get mine fixed, but that is because it took 6 weeks for the problem to act up so it could be traced down. This does not seem to be the case for you as it happens quite often.
In any case.....
Good luck!