I think the problem is caused because you expect the application you want to run, to run interactively with the desktop. In order for a service to start processes which interact with the desktop, the service needs to be configured to run in the system account security context and the check box 'Allow service to interact with desktop' needs to be selected.
Here's where the problem is. TopTools, in order to be able to extended discoveries in Windows NT domains, needs a security context with network credentials. The system account does not have these network credentials and can therefore not be used to logon to machines remotely to access information such as information available through WMI/WBEM, cluster configuration information etc.
So, the reason why net send works, is because you don't have to see the net send command executing to see the pop-up message on your screen. This is because the messenger service, which receives the message, takes care of displaying it. However, if you are just running a program, like cmd.exe, you will not see it because the HP TopTools service is not configured for interactive access to the desktop. You will find, however, that cmd.exe is actually running. It's just not visible.
So my advice to you is: only run programs which do not require interaction with the desktop. Also make sure that these programs terminate after performing their task.
Hello Ville, Here is the help information in Toptools about command line action on alerts: ???If you use a command line to respond to an alert, enter the path of the desired program for each alert severity. You can use a batch file in this field to launch several programs. The toptools server system will execute the command. The program and path must be on the toptools server system. Note that you cannot run interactive programs using this feature.??? This last line is where you are having the issue, as Erwin stated. Louis