So, today I've started up my computer and sometimes found a command prompt (or even multiple ones ) to pop up for a split second. I thought it was a windows thing.. The reason: It's already a really long time that I occassionally see a Windows Powershell Window pop up in the taskbar (the window itself is invisible). When I hover over it, it says something like "Administrator: System WoW64" I can't tell exactly, since I can't remember too well. Anyway, I of course scanned with Malwarebytes to check, but it didn't find anything. Since Powershell is quite new I figured it would be fine. Till today. Malwarebytes found exactly 40 programs that it had to remove, many of them being PuP and some being plain Malware. Mostly things that were DNS changers.
I want to point out that I didn't install any Software today! The last software I installed was a Corsair Gaming Mouse configurator, which I downloaded from the official website about a week ago. I have only had a single Malware incident on this computer before, which was when I accidently downloaded software from a domain, which has actually been a third party distributor. Of course, it cursed my computer with a bunch of PuP, which Malwarebytes removed for me. Afterwards I removed the programm and reinstalled it form the official source. (At least I hope I actually did that. I do use the Software occassionally.)
Does anyone have an idea what really happened in this incident, and most importantly, what I can do now to be sure everything is somewhat clean? I would love to search through my registry manually too, but I am not sure where and how to start. There certainly are many keys there..