Thanks for the responses. I managed to get it to work out after all. The only thing I could think of that I was doing wrong is when I was creating a new bone and the previous one was moving to line up that when I hit undo to return it to its normal position I screwed it up. I didn't touch the undo this time and it worked. 
I too do as little work in the setup room as possible. Is it actually possible to save your progress in the setup room without leaving it? I have just been saving the unfinished rig in the library and then reapplying it to the base mesh in order to save in increments.