I guess the only things left are either permissions, or something outside Openhab holding the GPIO Pins, or a hardware fault.
I run Openhab as Root which might be worth temporarily trying. I also installed Jessie as a new install, maybe its worthwhile getting a new clean image of Jessie + Java + OH and seeing if that works. A quick google suggests there may be permissions issues with GPIO after upgrading to Jessie from Wheezy.
If I had this problem I’d get a new SD Card and create my own image of Jessie, then test GPIO, then add Java & OH 1.8 then test again. Interestingly enough there is work being done elsewhere on the forum creating OpenHabian openHABian hassle-free openHAB Setup and the last post asks about getting GPIO to work so perhaps there is an issue that is about to be documented on that thread.
