It appears that special pages defined as inheriting from 'IncludableSpecialPage', and then embedded within another page, don't get their Javascript loaded correctly. The extension Semantic Forms defines such a special page, 'RunQuery', and you can see the problem when trying to press the button here:
http://discoursedb.org/wiki/RunQuery_embed_test
Here, by contrast, is the same page when not embedded:
http://discoursedb.org/wiki/Special:RunQuery/Author
If you look at the HTML source for the two pages, in the former page the Javascript resources that the special page loads are missing.
This problem seems to have been in effect since at least MediaWiki 1.16.
I looked into it a little, and it looks like the problem comes about because, when the special page is embedded, the OutputPage object that gets displayed to the screen is different from the $wgOut that the special page adds its Javascript to.
Version: unspecified
Severity: enhancement
URL: http://discoursedb.org/wiki/RunQuery_embed_test