Ok, now I see what is going on, I was thinking that I might have to change htaccess because of what I am doing with my wordpress install, but I have forgotten about doing it.
No, I have not switched between subDOMAIN and subFOLDER, I am still curently using subDOMAIN, but what I am doing is:
I am hosting several top level domains on one multisite install without using domain mapping plugin. I accomplish this by:
Whenever I create a new site in WP, it looks like this:
but what I do after site creation is, I go to site settings and I manually change:
All top level domains worked fine, except for upload issues and issues with "nice" URL's. (Default permalinks worked OK)
But now that I use subFOLDER htaccess for my funky subDOMAIN install, everything works fine.
Only if I have acted on my first thought of using subFOLDER htaccess few months back, I would have saved myself a lot of frustration. But I guess I am starting to forget things in my old age :)