OK, I've seen something similar on SnapManager for Exchange.
In that case the actual reason was fairly simple (& easy to cure): during installation SME asks which licensing model should be used, so if there is a license on the filer, that box should be ticked, not the other saying server license.
I'd simply try reinstaling SMSQL carefuly looking for questions about licences location.
Like the previous posts said, this definitely sound like when you installed SNAP Manager you entered the license incorrectly or you selected the wrong License Method. Our license's are all entered manually so during SNAP Manger installation I enter them and do not get them from the filer itself. Take a look under your licenses when you login to NOW.Netapp site and see if you have individual license keys for your snap manager product. It should be listed under Serial and Licenses when you log in to support. Good Luck!