Remford
I had a very similar problem with my factory cross rails I ordered from my dealer. They would just never fit right so I returned them and saved some money.

I went with the Thule Cross Rails and I really like them. I just take them off with the basket when I don't need them. Plus they lock. I have had them for about two years now and they have worked great.

Here are a couple of picts.

 

I bought the cross rails from the dealer when I purchased my 2006. I have had no problems. I paid approximately $300.