I had an InstallShield 2011 project (A) that installs a service, and copied this project to use for another project (B) that installs a different service.
During uninstall, it seems like if either (A) or (B) is installed, the service uninstalls and is removed from the Services list. However, if BOTH (A) and (B), then (B) is not being removed from the Services list on uninstall. The actual files are being deleted, so when I right click to Start the service, it says that the file could not be found.
I updated the Product Code and Upgrade Code on the General Information page of the project, and updated the Key Name in Setup Design - Advanced Settings - Services - [My Service] when copying the InstallShield project.
Are there any other shared items that could be affecting the uninstall?
The component GUIDs could be shared too. This is most likely the source of your problems. As a practice, you should NEVER copy a project and use to create a setup project for another similar product, this is the easiest way to miss updating some GUIDs that must be unique and have your packages behave incorrectly.
I don't know if InstallShield has the option, other tools do have it, but the recommended method is to create a project template from the first one (A), then create a new project from that template, case in which IS should make sure that you get new unique GUIDs for all sensitive areas from the package.