I've tried popup footnotes a few times and it works ok. Do you have an ePub 3 with anchors marked as
Code:
<a epub:type="noteref …>
and notes marked as
Code:
<aside epub:type="footnote" …
? I would guess that popups are supported only for ePub 3.
I'm aware ePub 3 support is preliminary. One thing about that, I'm not sure if it's in the spec, but using iBooks, the aside notes are not shown inline in the text. They're often included at the end of a chapter file or end of a section, and hiding them would be nice.