What causes it, and how do I fix it?
Anyone else have this problem?

The cooling system on mr2's is small... I find every now and then if I drive hard for half an hour or more and boost hard within about 2 minutes of stopping I'll get the telltale glugging sound. However as long as I drive normally for a few minutes after hard driving to help it cool the car doesn't seem to mind whether it's 15 or 40 degrees outside.

If you are referring to removing the coolant cap and it's boiling, that is normal. (Unless you have an inconsistent mix of coolant to water ratio).
If you are referring to you shutting off the engine and leaving the key on reds then the tempurature gauge shoots up, then you have another issue. Sounding electrical issue (temperature gauge earthing on reds).
Good care for your cooling system; If you replace the thermostat, have a radiator with no leaks (even small leaks can cause issues), flush / clean the cooling system (age of the system needs a little love), ensure no air in the system (follow the BGB to bleeding the air), and use Toyota red coolant at the recommended ratio; you shouldn't have heat issues....
I have driven hard on 40 plus degree day for hours, to the point of the aftermarket manifold cracking, however temperature gauge / temp is fine.

I do have all the heat items in place like intercooler fan on, rain shield removed (don't drive in the rain), heat shield on manifold, wrapping on intercooler pipes, larger intercooler.

OK, yes it's only bubling after shut of. The temp gauge seems to work and it never goes past just before half. It's not boiling while running. I have side mount inter cooler with fan on all the time and tad fans on all the time. I might have to set turbo timer for a bit longer.