First, be sure that you have updated the current Addon Manager because, if you still an old version, you are still on the original Cloud9 activation policy, which was 6 per order.
Also, you should confuse the number of *activations*, which is now 6 and is related to hardware changes, with the number of *server-assisted-Reinstall*, which is 3 and it's NOT related to hardware changes.
The current version of the Addon Manager will lessen the change for confusion, because during the Reinstall, it will ask only the Serial Number, that checks against the activations left, and not your Order Number anymore, that triggered a server-assisted-Reinstall.
So, first try to update the Addon Manager for FS9 to the current version, and see if you get that message again.
If yes, it means you really used all your activations, so you need to contact support via email, to get a new one.