Hey Mrgreen09, I did experience this and wondered if others would as well. I fussed with it for hours and here's how I ended up fixing it:
Under Super Admin, go to Sites and "edit" your secondary blog (is your primary blog's uploading functionality still working fine?).
Make sure your "Home" field is:
Your upload path is:
Your upload URL path is:
Your FileUpload URL path is:
Then, I went back to the "Network" link under Tools, copied the web.config info again and pasted it back into my web.config file and that fixed it. Even after I made the changes to my upload URLs, the paths didn't work until I copied and pasted the web.config info over again. Of course, this makes zero sense because the web.config code I started with and the web.config I ended up with are EXACTLY the same, but I'm chalking it up to internet magic.
Give it a try and if that works, I'll include this in my tutorial even though it's not very scientific.