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Remote Apps not allowing server side startup items to run

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Another day, another problem =).

This one is with Remote Apps on "Server 2012 R2".  We host an accounting software suite on a server and the users are connecting to it via Remote App.  Pretty standard stuff.  

The problem we are facing is that this program requires a companion program that runs in the background and assists with credit card transactions.  This companion is a completely separate program that gets installed per user using a "Clickonce" install.  It then runs automatically whenever the user logs in.  However, if the user logs in via RemoteApp using Seamless Mode, none of the programs set to run will ever start up and they get errors saying that the required program is not running.

I have already tried a load of solutions and none of them have worked.

1.  Set up scheduled task to run program when user logs in

2. Set up logon script within Group Policy for all user (windows settings\scripts)

3. Specified programs to runat logon under Group Policy (administrative Template\system\logon) under both comptuer and user management

4. Set logon script within user's account on domain controller

So far none of these have worked.  I know I can create a script that starts the program, then start the accounting software and publish it to the Portal, but I was hoping not to use that method.  I've also suggested publishing the companion to the portal, but it would require them to run it manually.

Thoughts?


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