Comment 2 for bug 1416526

There are no pages in ebooks. When you close or open the footnote panel,
the size of the text window changes, this means all the text has to be
reflowed into new virtual pages, so it is not possible to preserve the
original page. One could argue that the sequence of open footnote
window, then close footnote window should be idempotent, but trying to
implement that is fraught with problems, because one then has to
robustly handle the case of changes in current page or unrelated window
resizes/font size changes/resize of other docked panels, etc. between
opening and closing the footnote popup -- all of which can invalidate
the saved before footnote page position.

You should leave the popup window open, or if you dont like that, make
it a floating window, instead of a docked one.

 status wontfix