I never used the default-workspace to save real projects.
I can confirm, that it does not work as you do it.
Can you try it with "Settings->Environment->Open blank workspace" and open the project directly or use a "real" workspace ?
At the moment I do not have the power to work on the default workspace stuff.
I'm even not sure if I will be able to build a new nightly this weekend, too much work the last weeks, too much private stuff that takes precedence, sorry.