Here's a cool issue recently uncovered by Paul Freitas, one of our Support Engineers for MS App Virtualization. I hadn't come across this error before but if you see it this may be a good thing to check.
Issue: When an application is installed locally it runs fine, although when it's virtualized (sequenced) it generates the following error when launched:
Resolve Partial Assembly failed
Cause: This may occur if the same version of .NET Framework is installed locally as well as virtualized along with the application in the same package.
Resolution: The resolution is pretty obvious but I'll spell it out anyway - You need to either remove .NET Framework from the sequence or remove it from the client. Either way will work.
Links: Just in case you're looking for the .NET Framework packages you can find them here:
Hopefully you won't run into this issue during your sequencing adventures but if you do be sure to check this out.
J.C. Hornbeck | Manageability Knowledge Engineer