Hi,
I've been lurking for awhile and felt I needed to join now because I have been scratching my head with the same problem and I wonder if it has anything to do with Repap configurator, under z probe I have switch selected because if not the Z stop endstop is greyed out, I have had it set like this since I bought my Duet Wifi in March but i think it is in only the last two or three weeks that this problem has arisen and like the op I have been baby stepping my way out of trouble each print and the amount was always different, I actually got somewhere tonight after playing with auto bed compensation and getting nowhere I hit the disable button and levelled my bed manually as usual and started a print, a babystep of 0.3mm upwards and the print was going fine, i tried starting the same print again and left the 0.3mm baby step in, interestingly I had to increase to 0.6mm for the print to start, a 3rd print and I had to increase to 0.9mm for the print to start, in reality it was just the original 0.3mm I was babystepping and assume it just a display thing, I restarted my printer from cold and happily only had to babystep the 0.3mm again for my print to start, believe me this is the first time that I have had predictable behaviour at the start of a print for about three weeks, Im sorry for posting a wall of txt and I hope this can help the op out, please dont ask me to start posting loads of lists of g codes because i'm only a beginner really.

One more piece of info that may help, on Reprap config I have Trigger height at Axis and Trigger height on bed: set at 0.5mm