Hey CountryBumkin, good to hear from you.

My guess is you have a suction side air leak and you are losing prime. If it happened only when you switched to the vacuum, I would think the leak is within that system BEFORE the pump. As an example, if your vacuum hose floats and has a small leak, when it is not in use it can fill up with air, and then when your pump switches over to vacuum, all that air will cause the pump to loose its prime.

However, since it also happened when you were on the main drain/skimmer, it is likely the pump or any lines the vacuum and main line share, such as the line going into the pump, or the valve. Check the basket lid gasket and valve gasket, if they are worn or old replace them, if not apply some lubricant and replace, see if that helps.