I have successfully created a trigger to look for a running application... in this case we will call it program.exe. The trigger works and alerts go out. I'm trying to have a remote command go out in attempt that the agent server will fix itself.

So I have a bat file named "program.bat" on the agent server that has the following in it:
@echo off
start "" "C:\Users\Winbin\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\ProgramName\program.exe"
exit
The bat file does exactly what it needs to do on the agent server. However when executed remotely it does absolutely nothing. 

I ran it in command line on the zabbix host to make sure it connects
zabbix_get -s IP -p 10050 -k "system.run[C:\program.bat]"
and it seems to do it... but the application doesn't start on the agent machine

notes:

EnableRemoteCommands=1