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 04-0000041EEvent:
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
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.
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"
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!