I had the same issue and realised that my version of XBMC is serving using Library mode by default currently - and chances are you are too.
So - try this; you'll want to include the files in your library this way:
*In xbmc, select 'videos'. Add source, choose a videos folder and give it a name.
*Right click your new video folder. Set content. I've chosen 'movies'. Click a 'scraper' (such as IMBD).
*Select 'run automated scan' and 'Scan recursively' if you have multilevel folders.
*Select 'OK' and your video files will now be added to the library.
More information here:
http://wiki.xbmc.org/index.php?title=Video_Library
For Audio, from XBMC home, select 'Music', add source, choose a music folder and give it a name. Right click the folder and select 'scan items to library'.
Now, when I hit with the iPad2 or the Android device running Skifta, I pick up all the library items.
Let me know how you get on!