Originally I disabled all the protection, then started up the game to see if it was fixed and it was.
I just started up the game to test, and found out that after I stopped playing and re-enabled all the protections the game worked fine. No lag on autosaves.
I then restarted my computer and started up Borderlands 2 with all of Malwarebytes protection starting on startup and found that the lagging on autosave was back.
I proceeded to check each option, one at a time, off while leaving the rest on, then turning it back on after turning it off didn't fix the lag.
I have found that disabling Ransomware Protection fixes the lag on autosaves.
Re-enabling the setting after disabling once, does NOT bring the lag on autosave back. I must restart my computer and have the protections begin on startup for the issue to reappear.