I noticed that after installing cdt, Eclipse always loads the default workspace. The workspace listed in the config.ini in osgi.instance.area.default
config.ini
osgi.instance.area.default
Aptana 3.2.2
\configuration.settings\org.eclipse.ui.ide.prefs
Edit:
RECENT_WORKSPACES=I\:\\PDT\\workspace
It will check the recent workspace, so just set it to what you want, I do it for running off external drive.