Actually, I know what the problem is - I was previously playing on version 3.8. There were no micro-freezes; everything ran smoothly.
I recently updated SPT-AKI to the latest version, and the freezes started immediately. I've tried changing every possible setting, and nothing helps.
I only have 2 mods installed: Backdoor Bandit and Boss Tracker, which is even fewer than before.
It seems the issue is with the changed profile progress saving system. Previously, the raid result was loaded at the end, after exiting the raid. Now it happens during the raid, and the CPU is under a very heavy load—so much so that the rest of the system struggles to function.
Is there a setting to change the profile save mode?