HI Marc and Rouslan,
I tried on your demo server and as far as I can tell the tooltips are
completely broken now. They are no longer generated for the normal page (but the footnotes are hidden) and they don't appear in the ajax dialog (the footnotes, again, are gone though) (ubuntu 11.04/firefox 5).
Also as Marc said, with the code that you committed you would be generating duplicate IDs, I suggest you merely change those to classes to avoid possible conflicts (or you could come up with some scheme for generating unique IDs, though that sounds more complicated than is necessary).
I'm very sorry that earlier I made the wrong changes to the initTooltips
function. I fixed the issues and pushed to the repo. Please check that. Thank you.
Regards, Thilanka.