I've been unhappy with Scottrade too. I recently opened a Zecco account. Zecco's site is slow and the free tools are terrible. But, they're cheap and I can buy anything!
I think it's possible that Scottrade allowed shares to be used for shorting. All I'm saying is that I don't think they're communicating with MM's, but each party is acting in its own interest, and sometimes they align.