I haven give it a try. And it looks ok for me.
Please don't laught, I am not (yet) used to work with this bug tracking and open source programming environment. I did the following:
(1) followed your link to the "version" 4c5a5d3d
(2) clicked on source to see the file strucutre
(3) navigated to "dokuwiki / lib / scripts / script.js"
(4) did not find a way to download the file with your bug fix. Btw: can you point me to a place where I can find instructions on how to work with the system properly? what did you actually expect me to do to test you proposed fix? to download the complete new set of files?
(5) clicked "raw"
(6) copied the displayed text into notepad++ and saved as script.js
(7) renamed "my" DokuWiki's scripts.js to scripts.js.org
(8) copied the new script.js to my DokuWiki installation
(9) started the wiki
(10) opened the page with the footnotes
(11) didn't see any change in behaviour at first, hit refresh button of my brouwser and was then able to produce the encouraging result as shown in the attached file.
Result as I see it: the footnote popups now appear below and slightly to the right of the clicked footnot indicator (in the picture, I clicked on indicator (1) and (15) as in the original post), i.e. I no longer see a strange displacement of the pop-up relative to the footnote indicator.
I saw this improved behaviour both on MSIE 8 and Safari/iPad. My DokuWiki uses the VECTOR template.
Thanks for the fix!