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Hello,
I have verified that the cloning process seems to work as expected. I have tried it here on my own machine, and all copies of "imenu" are changed.
Since the clones do not work when they are appearing on the screen together, but they do work when they appear separately, all I can say is, do they have different names?
If you made a two clones with the same name, they could not interact.
The names need to be different.
I'm sorry I can't say more. There is almost certainly a fatal error in PHP, and if you can get your website to tell you what the fatal error is, then this will be easy to track down. You should look up information about how to get PHP to show you all the errors that happen. This is not a simple thing, since many web servers are configured to hide fatal level errors from users.
--Julian