The issue is resolved. For anyone arriving at this page from Google, I am sorry to say I don't know why.
While I had done absolutely nothing in my Netduino, connecting with MFDeploy again suddenly showed the options as unlocked. I haven't done anything or changed anything to either my PC or the board, yet something seems to have happened and now it's working perfectly. Excellent for me, not so great for actually understanding the issue.
So, in short, problem solved but I don't know why.