My first test would be to capture the application while doing a normal, manual installation. Not using the SCCM deployment.
What is showing the invalid MSI? Is it View administrator is it probably due to something mentioned here: http://blogs.vmware.com/thinapp/2011/03/invalid-msi-and-why.html
Can you, please, post Package.ini file?
I have used this linked before. I have tried all 3 options and still no luck. I am not sure how to answer your question below...
"What is showing the invalid MSI?"
(The EXEs/DAT and MSI files are all located in the \bin directory by default, so I am not sure why this is #1 on the checklist within that link you provided me.)