In the past week I've gotten a few emails from folks working with the file system in PhoneGap/Cordova apps. Recently, the plugin had a major update and if you weren't paying attention to the docs/blogs, it would be easy to miss.
First, see the blog post from the Cordova site: Plugins Release: Feb 10, 2014. Second - you can get even deeper docs at the plugin Github repo docs: Docs. Finally, as the changes here were intended to bring the plugin closer to the core HTML5 FileSystem API, you should refresh your memory with the excellent HTML5Rocks article and the official spec as well.
I started up a fresh project for iOS and had no problem accessing the file system, but I didn't do anything too complex. If folks want to talk specifics, I can try to create a specific demo, but again, I strongly recommend reading the plugin doc.