SQL Comparison SDK (formerly Toolkit) applications are licensed at build-time. If you do a build in Visual Studio and have included the licenses.licx file as an embedded resource according to the instructions, then you [b]will] get a nag requester at that time and you can click the button to enter your serial number and each subsequent build should licence silently.
If your compiled assembly nags the end user, then the licensing probably didn't work.
This is the section of the product help that deals specifically with the licensing:
http://www.red-gate.com/supportcenter/C ... c68944.htm