I just posted an article about how to do this:
Let me know if it's useful to you!
The link mentions a problem with updating an existing an FMP13 instance using Group Policies -- I've had the same problem. Adding the FMP13 update to the GPO successfully updates instances that were already installed, but breaks the ability to install from scratch. Since we wipe and redeploy any machines with issues, it defeats the purpose to have to reinstall those from scratch -- it basically means the GPO is only useful the one time, for the initial upgrade of installed machines, and after that is useless.
Anyone have any ideas on how to get the base file *and* the update to both install properly from GPO? The best "solution" I've gotten so far is to re-ask FM for a download link to the full installer every time an update goes out. Obviously not ideal for anyone.
I think the issue is with installing the base app and then the patch in the right order or with enough delay for the computer to figure out that FMP is already installed before trying the update.
If you set the update to not uninstall when the program is removed from the GPO you can remove it without affecting the other programs, so you can temporarily remove it, install the base through GPO on the new machine, and then put the patch back in later. That's the best solution I've found far, though I'm sure someone more familiar with GPO details can offer a better solution.
I hope we can find a better solution -- disabling the option to uninstall when a machine is removed from a GPO makes license management through GPOs pretty much impossible.
I'm not 100% certain, but I feel pretty sure that last time I checked, I looked at the MSI installer logs on one of the failing machines and it seemed like the base app wasn't even trying to install once the upgrade was put into the GPO. I just assumed this was expected behavior for GPO updates -- that the GPO expected to install only the update file.