This may be obvious to others, but I was having some problems with not being able to control how I logged into SharePoint Designer. I have a couple of accounts – one for normal work, and one with admin privileges. What I found was that SharePoint designer would log in variously with one or the other of these user accounts, without any obvious way of amending it to log in with the other account.
The solution was to go to Internet options, and remove my sharepoint site from the trusted zone. This requires me to log in to the sharepoint site with IE (i.e. not automatically from my domain login), and SharePoint Designer shares this behaviour.