Different Kind of Permalink Issue

So..my website has been up and running for nearly a week, no problem. Last night, I changed a link (a link that points outside my website) and uploaded index.php. I went to test the code, and all my permalinks were broken.

I don’t use custom permalinks..I deal with the ?p=2 stuff.

Any links ending with ?something just point back to the root directiory.

I’ve deleted index.php, and it points to the root directory.

I’ve also deleted htaccess and tried setting custom permalinks.

It’s all the same. Just points to the root directory.

Any ideas?