Hi
I have chosen "Generate instance at installation time" option and done some other things like Navigation of folder tree, verified the custom action and the config file updates etc and again chooses the menu Multiple Instances but the "Generate instance at installation time" option was not checked. But I couldn't replicate this issue again.
Also in the newer version of the AI(after 11.6) the "Generate instance at installation time" option is not getting saved. Each and every build we have to select this option for supporting the multiple instances.
Please have a look into this issue