SEO titles have stopped working.

So last week I was having problems with the site adding a variant to one of my options. CS-support told me I needed to changes some of my permissions. I changed them but was still having some issues so I contacted my host (Secure Cart Hosting) and they said they permissions should NOT be set at what CS told me.

Anyway, after my host played around with some things we got the site functioning properly again. Or so I thought. I noticed last night that all my internal links within CS are now not SEO friendly. They always were before. The search friendly links still work because Google is still showing the old links. But I nor my host can figure out why the internal links have stopped being SEO friendly now.

Help Please!!!

The site is for reference.