How did you pin it to the taskbar?
Edit : Actually I think I have worked it out.
If you pin it from the start menu (either Start11 OR the windows one) it will be pinned to the taskbar, but when run it will show a second button on the taskbar. This happens without Start11 too.
The solution here is to not pin via the start menu, but instead run the app and then right click the running app and pin that to the taskbar.
Unfortunately this looks like an issue with the shortcuts created by their installer not having the appID set on them correctly which is why it happens with and without Start11.