Had the exact same problem, and was driving me crazy after trying to use Sugar.
However, someone suggested to disable Compiz in the forums for an issue with mouse poling while he was using a program, so it gave me the idea to try disabling Compiz and see what happens.
After doing so, my mouse worked normally again, so I narrowed it down to Compiz.
Then I went all around Compiz settings, until I finally found the culprit in the General Options, Key bindings for Window Menu.
Just to make things short, you can access it directly through gconf:
Hi,
Had the exact same problem, and was driving me crazy after trying to use Sugar.
However, someone suggested to disable Compiz in the forums for an issue with mouse poling while he was using a program, so it gave me the idea to try disabling Compiz and see what happens.
After doing so, my mouse worked normally again, so I narrowed it down to Compiz.
Then I went all around Compiz settings, until I finally found the culprit in the General Options, Key bindings for Window Menu.
Just to make things short, you can access it directly through gconf:
/apps/compizcon fig/profiles/ Default/ general/ allscreens/ options/ window_ menu_button
Change setting from "Button3" to "<Alt>Button3" (Without quotes of course)
Hope this helps.
Question still remains. Why does Sugar change this setting?