While upgrading our 220.127.116.11 version to 9.6, we hit an issue were the "Target installation directory:" behaved differently when using the browse versus manually typing in the directory.
When we used the browse button, and continued with the install, the version was not detected. The effect of this was all of our configuration files were not kept/upgraded but were replaced with the default configuration set.
We then pulled back the system backup of before we started the upgrade and went through the process again, using the browse button again. We recieved the same behavior that the EM was a clean install instead of a upgrade.
Third time is a charm, right?
We pulled back the system backup again and by chance manually entered the the target installation directory and the upgrade detected our 9.1.1 install and completed without overwritting our 18.104.22.168 configuration.
Hope this helps,