the free account can only be used on two devices at the same time. In order to unlink a device you have to either sign out in the software or unlink the device from the web interface. I assume you did not sign out before you reinstalled and thus the old installation is still linked to your account.
To resolve this, go to https://www.boxcryptor.com/app and sign in. Then go to the Devices page and unlink the old device.