Hi,
I haven't tested this since I don't have this application but I would recommend to use the msi file (the is a lot of advantages to this). WHat they are doing in the setup.ini, you should add in the parameter windows in SCE. To do this I would:
1) Start the Add New Software wizard in SCE
2) Brows to the msi file
3) In the parameter windows, add SERIALNUMBER= XXXXXXXX
4) Add/configure the application.xml as you want it
5) Test
Björn Axéll MVP - Advisec AB
http://blog.advisec.com