I'm running a test print and pause/resume is working correctly now. That was the problem. Replacing the G1 R1 in resume.g with G1 R1 X0 Y0 Z0 fixed the problem. Thanks Dave!
Checked after power cycle, printer appears to be functioning again. I did do a M502 and M500 after upgrade that might have done something to create the issue.
What's happening is that the voltage at the VIN terminals on the Due is dropping when the bed heater turns on. This can be caused by any or all of the following:
The output voltage of the power supply is not well-regulated. This is a common problem when using cheap ATX power supplies.
The cables connecting the power supply to the Duet are too long and thin
The screws in the VIN terminal block are not tight
At those prices I'd say that you aren't using genuine parts as supplied by from RepRap.me and with genuine E3D heat sinks. TBH and without wishing to cause any offence, that may be why you have problems. If you are interested, I did a bit of write up on my blog on how I assemble Diamonds hot ends. I don't seem to get the blockages or leaks that most people complain about so you might find something useful in what I have written - https://somei3deas.wordpress.com/2017/05/28/how-i-assemble-diamond-hot-ends/
Update - This combo is working very well for me now with the latest Duet WiFi firmware updates (>v1.19). I especially like having macros for the BLTouch and probing calibration points on the bed.