Go to Preferences, to the General pane. There's a button at the bottom that says "Reset All Warning Dialogs". Push that and see if it helps (you may have to restart InDesign).
I did try resetting the dialogs, but no avail, but, but...
Suitcase Fusion appears to be the evil-doer, the new Fusion 5 (which I was trying out) plugin was activated, no warning dialog. After disabling the 'auto-activation' the dialog reappeared!
This happened in CS 5.5 and CS 6 (and also the CC tryout), so off to the Extensis forum with this one!
Extensis is working on addressing this issue in an upcoming SF5 v16.0.1 patch.
Extensis Product Team
A free update to Suitcase Fusion v16.0.1 will be available for download on Monday, August 5th. This issue has been addressed.
Please let us know if you experience any remaining problems after upgrading.
Extensis Font Management Team