After installing the most recent update to STS 3.9.0, my Ctrl+Shift+O keyboard to Organize Imports is no longer working. The key shortcut exists in Preferences->General->Keys ("Keys" preferences) but is missing in the Source menu ("Source" menu).
This is a bug. You can workaround it by fixing the Eclipse shortcut keys preferences.
From the bug report:
here is how you can fix that issue:
Go to the Preferences -> General -> Keys press Filters... and de-select Filter uncategorized commands. Look for the command "Go To Symbol in File" and select that, press unbind and Apply and Close