I have the same issue on vita slim. After disassembly totally change the main board to another vita slim, and the problem do not occur in the same way.
Exemple:
1- in the original vita slim with this problem, it only shows when some application uses GPU, like a game or a app using FTP (Vitashell).
2- After change the main board to 2nd vita slim, game plays well for some time, like 2 or 3 minutes and after that it hangs and show error saying it will "....shutdown [******]"
3- Replace back all pieces to vitas, reinstall firmware via safemode (on the problematic one), but after install fresh new firmware issue continues.