When multiple instances of the update checker are active at the same time, each will have its own PluginUpdateCheckerPanel instance and its own entry in the Debug Bar. However, since all instances have the same class name, and Debug Bar uses this name to generate link and wrapper IDs, we will end up with duplicate IDs and a semi-broken debug bar.
I've added a bit of JS that will find update checker panels and replace the relevant IDs with new ones based on the plugin slug, not class.
Yahnis Elsts