I am using Advanced Installer to author the MSI but this issue should be standard to MSIs in general.
To avoid the headaches of having to uninstall\reinstall MSI packages every time I want to make a config change I have an MSI that removes all previous versions (via a custom action to execute wmic product where name="NAME_HERE" uninstall)
The MSI sets registry keys (that the underlying services uses) upon installation. My goal with re-pushing the MSI is solely to update the keys (if I make changes to the Property table w\ Orca) but the problem is the keys are not updating. When I run the msi with
msiexec /package INSTALL.msi /lv* C:\install.log
I notice when the MSI loads the propertys they are the same as what was previously installed, not what has been altered in Orca. The only way get the new registry keys to reflect is to uninstall\reinstall the MSI.
EDIT: It appears to be taking the properties of the MSI that's cached in C:\WINDOWS\Installer