Okay I've been playing around with it a bit more and reverted to Ediabas 6.4.3 and I think is working better, when the OBD is not connected I get error IFH-0003 and when its connected to the Mini I get IFH-0009, so I'm guessing its the wrong lead for the R56?

This is the lead here:

http://www.ebay.ie/itm/BMW-USB-Diagnostics-OBD-Cable-Interface-lead-Ediabas-Inpa-DIS-SSS-Progman-GT1-/151210282258?