Actually, as I think about it again, if your user logs out before logging in, all of the sequences should close. If you just go to log in without logging out, as it seems is the case with your situation, you will need to add a step to close open sequences. This can be accomplished by placing an ActiveX action step after the login step of the FrontEndCallbacks sequence (which can be found at <teststand>\components\ni\callbacks\frontend). The automation server will be "NI TestStand API 4.0 (or whatever your version)", the object reference will be runstate.thread, the class will be thread, the action will be Call Method, and the method will be PostUIMessage. The event code will then be UIMsg_CloseWindows, the numericDataParam will be 0, the stringDataParam will be "", and synchronous will be False. Then go to the properties of the Login step, and edit the Post Action so that On Condition True, you go to the ActiveX action step you just created. Let me know if this does not seem to match your needs, or if you have any other questions!
NickB