 Caleb,  I believe your issue is due to group policies on the TS, specifically ones preventing applications to launch on login.
Hi guys,  I've had success publishing full desktops with vWorkspace and it works great however I've been dabbling in the seamless windowed application for a side project. I've got the application working fine from the Full published desktop but when it's published directly into a user's application list it doesn't start...  The client splash window opens and does nothing, and when I click Details... the session is sitting in the full desktop, albeit in a reduced side.  Any ideas?
Seamless Application not starting