check the workspace setting under FB->Preferences->General->startup and shutdown ->workspaces
The checkbox 'prompt for workspace should be unchecked" and look at the number of remembered workspaces.
You can remove the workspaces you dont want.
If still you find that flash builder is not saving the correct workspaces in preference, please log a bug at https://bugs.adobe.com/flex/
First of all, thanks for your help. I have been asking around with this problem for about a week without a solution.
I tried changing the preferences but that did not seem to work. Then I tried to register with the link you provided, but apparently I do not have permission to post a bug (maybe this is because I used my home email address but I'm using the software at work??)
did u register to the site? if yes then you should be able to log a bug.
make sure to attach logs and screen shot for the above preference page to the bug.
we could see this issue in 4.0.1 build.
Can you plz confirm which build you are using. In the latest build we dont see this issue anymore so looks like its fixed.