I believe the problem is:
Open C::B -> default workspace
Open a project -> workspace changed
Close the project -> doesn´t recognize the workspace is back to what it was on start
Close C::B -> tells you it wants to save the workspace
Helpful would be an option within the question, like "do not bother me again"
and once thats checked don´t check anymore for changed workspace upon close.
At least in my case there is no need at all to save anything at all upon close, I always click "No" and I´ve never determined anything missing that wasn´t saved.
Edit:
Now that I think about it, I believe, no matter what you save there, it still loads the default, so you don´t even get back what was saved, unless you load it manually.
If so, a 2nd option might be useful, like a checkbox saying "always save workspace as default"
Not sure if I explained it right, I mean it could auto-save upon close under a default name and auto-load it again upon open without the user has to click anywhere, and if thats optional, everyone may choose the way they like best.