I am correct in understanding that you used the 'Package Builder' Snapshot Wizard to create the package for this application?
It appears to be prompting for the original installation MSI the first time you run the application, which presumably isn't cached on your snapshot device after the installation has completed.
If the answer to my first question is yes, then did you try to run the application once when you were creating the package before you took the second snapshot.
This might allow the installation to finalise whatever it is trying to perform, I.E copy some extra files, update the registry using the original MSI source.
You could also add the MSI in question as an additional file to your distribution package and have it copied to %TEMP% or whatever the correct path is.
So if it was a snapshot as Blair indicated, this should be the last option for packaging. There are inherit issues with snapshots (excluding app virt snapshots), one of which is displayed in your post. I would try and use the vendor/s installation package where possible. The majority of packages can be installed without snapshots. You will then have a much cleaner install that is supported by the vendor.
It appears that this is a MSI so it should be able to installed as a MSI, without a snapshot or using package builder. IMO the time spent troubleshooting a product that is pretty much EOL, would be better spent learning/creating a new distribution package with the MSI.
Yep. Completely agree with Zman on this. You may have been using the package builder historically but I would also recommend migrating away from it to MSI distribution packages. The package builder tool is useful for small things like file copies, registry edit but i would leave it at that.