Have you tried going back to Cydia and reinstalling iFile? Once you uninstalled it/rebooted the iPad, maybe try again with the Cydia install? Did you use Cydia to UNinstall iFile? Sometimes, if you take it off yourself, without going through Cydia, you cause more problems for yourself. Hopefully, using Cydia to put it back on may re-load it right.
Honestly, that's all I can think of. And, I think it is iFile that's messing you up. So, unfortunately, unless you can get iFile to "behave," I'm afraid you are facing a restore.
Sorry, but I'm all out of options.