New
#11
This time clean install seems to have worked, so I can now install software the way I used to. I also deleted all unnecessary partitions on disk 1.
I was hoping to at least find the cause as I haven't encountered something like it before, but sometimes the quickest solution is the best. Again many thanks for the help, I will be marking this as solved.
(As an aside, I did try fiddling with the permissions, but had zero luck there so it was probably not the cause.)