The problem is in SkinMobile.php. 'position' => 'top' modules are packed into the $headModuleNames array and 'position' => 'bottom' are packed into $moduleNams. $headModuleNames are loaded properly and without fanfare, but there is some code hacking around ResourceLoader with $moduleNames (grep for '$bottomScripts') that (as far as I can determine) only works for 'raw' modules.
Version: unspecified
Severity: normal
URL: http://www.mediawiki.org/wiki/Manual:$wgResourceModules
See Also:
https://bugzilla.wikimedia.org/show_bug.cgi?id=44070