I had managed to sequence it fine but the package was taking an age to load up and sometimes timing out completely.
After looking at the SFTLOG (C:\ProgramData\Microsoft\Application Virtualization Client) I noticed an error: 4636126-0B01FD04-0000041E
As per AppV error format:
App-V Error 04-0000041E
Event:Starting/Running the application
Error Message / Symptoms:
It took to long until the application was ready for interaction with the users.
The application shuts down after about 5 minutes
Potential Causes:
The application is a Java or DOS like application. App-V can not determine that the application is ready for User Input, because the app does not use default Windows Classes.
Potential Solutions:
In the OSD file, SUBSYSTEM VALUE has to be changed from "windows" to "console" (case sensitive).
If it is an 16-bit application, also the VM VALUE should be set from "Win32" to "Win16"
References:
Microsoft Knowledgebase Article: http://support.microsoft.com/kb/931112. This articles lists a set of potential causes, however the most common reason (SUBSYSTEM "windows") is not listed there.
Thanks to Falko at Kirx.org for the above.
Once I'd made these changes I updated the package and viola, Bob's your aunties live-in lover!