I ran into this problem a little while back. This happens when you try to apply license keys to a Workgroup engine that runs as other user then Administrator on a Vista or Win7 machine. Here is what I did to fix it:
1. Log in to the computer as Local Administrator
2. Shut down the Workgroup Engine (w3dbsmgr.exe)
3. Run the Workgroup Engine as Administrator
4. Start the License Administration as Administrator
5. Enter the license key/s and hit ‘Apply’
After this I finally could add my permanent licenses for Pervasive Workgroup Engine v11 and DataExchange 4.