Is there anything i can do to over come this with the ecu in the car still?
Thanks
Software wise not that I know. But I also don't own a million different tools.
You need to get a direct K-Line from the ECU to the diagnostic connector.
This is also required for ME7Logger to work with certain clusters.
Though it is also very much possible reading is disabled in your file. Usually what I find with these is that you can start to read, and then it'll break up mid way.
I don't use the nefmoto flasher though.