I have this weird issue where the following happens:
I have exactly the same problem on OSX, for no reason, one fine day, Eclipse will start-up with a new blank workspace!
And to all the stupid answers and responders out there: YES I know how to set and select a default workspace! And NO creating a new workspace, re-importing lots of projects and loosing all my 30+ database connections under my Toad Extension, is not an option.
What I found is that
/Users/user_name/Documents/workspace which is the blank workspace it starts-up with (incorrectly)/Users/user_name/Documents/Development/eclipseThe solution is (this is on Mac OSX, don't know if it is the same on Windows):
/Applications/eclipse){eclipse_dir}/configuration open the file config.iniosgi.instance.area.default=@user.home/... and confirm that it is pointing to the bogus workspace directory.config.ini file..metadata directory (its hidden). Inside the .metadata directory, remove the .mylyn directory and restart Eclipse.This worked for Eclipse Juno.
Hope this helps!