Is the shortcut in question an advertised shortcut or a non-advertised shortcut?

What is the shortcut calling?

How did you place the MSI files into the layers?  

Try to Recapture the applicatin using below command line

Msiexec /i "path of MSI" transforms="path of MST" DISABLEADVTSHORTCUTS=1

you must *always* as EdT has pointed out, disable the creation of advertised shortcuts, also you *must* start all shorcuts, to ensure that no self-repair activites are attempted to be carried out once the virtual package has been deployed (as the source MSI will never be available). You *must* remove all MSI engine based information from the registy, i.e. Darwin descriptors, all msi information from the .Installer registry hives etc. Failure to do this means that you have a "defective" msi installed application in the virtual environment, and it's a bomb ticking, waiting to go off.

just my tuppence

"you must *always* as EdT has pointed out, disable the creation of advertised shortcuts, also you *must* start all shorcuts, to ensure that no self-repair activites are attempted to be carried out once the virtual package has been deployed (as the source MSI will never be available). You *must* remove all MSI engine based information from the registy, i.e. Darwin descriptors, all msi information from the .Installer registry hives etc. Failure to do this means that you have a "defective" msi installed application in the virtual environment, and it's a bomb ticking, waiting to go off."

This is all good advice and it sounds like XPF packagers should always be doing "all of the above". However, I'm also sure this involves a whole lot of manual steps, as Wise Virtual Composer does not automate all of this for you. Are the "how to" procedures for the above items documented anywhere under a KB or forum post?  Something like a "Best practices guide for capturing MSIs into Layers"? That would be hugely helpful.