Why are you running the jets with the cover on?
The jets do not have a programmed time on a HS that I know of. They have a time-out, meaning they automatically turn off after a certain time (usually 20-30 minutes) and will engage for short periods to recirculate the water a couple times a day, but the heat and primary filtration are on the small circulation pump. But then, I never see the new ones, so maybe they switched it up. But I can tell you that any spa pump ran on high speed (the only speed yours likely has) for 2 hours straight is going to get screaming hot, and will transfer some of that heat to the water. In a tub as well insulated and efficient as a HS (and there aren't many) it will be even more. If your spa is turning the jets on high for 2 hours automatically then that's a problem, but if you are leaving them on for 2 hours then that's on you. I would think the timeout would be less, but it varies with brand.
I didn't think so.
Really? I thought that vented to the outside. Seems rather foolish to dead-end your pump vent into sprayfoam after designing a motor to channel the forced air exhaust into a vent hose. Bet those motors get HOT.
You can. And that vent tube really should be taking heat away, not deadheading the vent blower in some ill-conceived plan to increase efficiency by a fraction of a percent. Dumping that heat into the equipment area, while a better option than a clogged vent hose, is not enough. Leave a side panel off to allow some airflow in that little box full of hot equipment and see what it does.
Define "running". If you mean "jets on" then that sounds about right. Especially with a dead-end vent. But if it's just with the circ pump on it's likely a circuit board issue.
The issue, I believe, is how long the high speed pumps run, and the weather is only disguising a symptom.
I know there have been some heat-related issues with a certain pump manufacturer, perhaps HS has changed suppliers and now have pumps that run hotter than before.