I'm trying to test an external program that will eventually email notifications to users when a refresh is finished. Currently I'm just testing a batch file named c:\test.bat that copies a file c:\test.txt to c:\test2.txt. Running the bat file from the command line works fine. But when I try to test run the External Program it just freezes, a Tokens.xml document appears in the c:\ directory and the web browser shows an hour glass and doesn't let me click any where else on the webpage? I have to restart all the services in order to get the web page to start responding again.
I know that this won't solve the basic problem (namely why an external batch freezes the server - if it really IS the server an not the browser ...), but if it's just for notification of users after a reload, perhaps you could (and should?) use the "Alert"-feature (On Post Reload). Maybe that's sufficient for your purposes.