An issue I've seen with SQL Server 2005 Management Studio (9.00.1399.00) for a while. I found a successful work-around for it which works fine, so I have not bothered looking for a 'real' solution (there may even be an official fix? But I don't care). Recently a friend asked me about this same problem, so I decided it might be worth posting on this super-duper information highway.

Anyway, the issue is that when we save a large diagram, the annimated disk icon (symbolic of "please wait while saving") seems to continue for however long you leave it, and the rest of the studio is froozen.

The Work-around
Minimise the management studio (either using the top button, or right-clicking on the task-bar item), and then maximise it again.... Walla; finished saving successfully, and no longer froozen.

Any other operation (ie, killing the process) I've tried results in loosing the data changes you're trying to save.