@dc42
In the spirit of science I am trying one change at a time. I connected the thermistor to the second input on the Daughter board and changed the firmware accordingly, I did not add the additional 2 wires. The temperature seems to be about right now as it prints nicely at 225 degrees. I suppose this indicates your suggestion that the converter chip is faulty. How do I go about fixing it as I will need the second channel soon once I have all the initial bugs worked out and add a second extruder?

Well thank you all for your help. With dc42 suggestion and Link to wiring diagram from T3P3Tony I have it fixed. I had the black and blue crossed. (So much for making black the standard ground or negative).
All is working as it should.

Cheers everyone.
Leif

Got replacement BL touch (First one was apparently faulty) and that has significantly improved things, still not perfect but almost acceptable.

I am going to rebuild with stout linear rails and with busy work schedule should be back at it in a couple months. Hopefully that might improve things.

@dc42
I'm using firmware 2.0(RTOS) (2018-06-05b3)

I Changed in the M558 the F320 to F120 and the result is better. Here is a screen shot.

Running another print with the mesh bed on and it is much better but still puts the nozzle into the bed in a few spots. Overall this is better than without mesh bed compensation but still not acceptable.

@phaedrux
When I do multiple mesh bed compensation the map turns out very consistent every time, so I would guess that the BL touch is consistent.
If I print with the mesh bed on it will push the nozzle into the bed in most areas of the bed. If I do a print with the mesh bed off it is much better but not perfect yet. I am printing on glass but so far have not been able to achieve what I would expect.
Here is the G code:
M558 P9 H5 F320 T6000 ; Set Z probe type to bltouch and the dive height + speeds
G31 P500 X14 Y35 Z0.92 ; Set Z probe trigger value, offset and trigger height

@phaedrux
When I move the nozzel across the bed with the mesh bed leveling on, the nozzle is slowly lifted from the bed. With the mesh bed off the nozzle keeps a consistent distance above the bed.

@dc42
I have a warranty daughter board comming.
Thanks for your help

Never mind about the first issue of printing at Z0.7. I was so focused on the firmware I did not notice that I had accidentally had a Z height offset in my slicer settings. Ah the silly things one does when they are frustrated and tired. This is one issue a good nights sleep fixed.

Still have the mesh bed issue.

I am using a BL Touch

I am having issue with the Z height changing at the beginning of my print.
In my start script I have a purge line set at Z0.2 Once this is complete the print head moves to start printing the part but lifts up to Z0.7 which is way to far for the first layer to stick properly. I have spent so much time looking through my config files I think i'm getting blind and missing something very obvious. I am using Simplify 3D as my slicer.

A second problem with mesh bed leveling as follows;
I manually set the Z height on all four corners of my bed so that the nozzle is the correct distance above the bed. When I run the mesh bed leveling it shows the right side of the bed is much higher than the left. If I manually lower the right side to get a more level mesh grid, the nozzle is over 2mm above the bed.

Here is a picture of the mesh bed with the bed leveled properly.

@dc42
In the spirit of science I am trying one change at a time. I connected the thermistor to the second input on the Daughter board and changed the firmware accordingly, I did not add the additional 2 wires. The temperature seems to be about right now as it prints nicely at 225 degrees. I suppose this indicates your suggestion that the converter chip is faulty. How do I go about fixing it as I will need the second channel soon once I have all the initial bugs worked out and add a second extruder?

Phaedrux
Unfortunately I only have PT100's all original E3D so I can't swap for a different kind. I have put in a spare pt100 and it has the same problem so I can eliminate a faulty PT100. I am running a 2 wire system but will try a 4 wire. I will look for a independent thermometer so I can check it from a completely different source ( hard to find such thermometer)

All PT100 are E3D and I am running the Duet Daughter board.

dc42
The PT100 is securely installed.
I am going to try the 4 wire system and following the directions you laid out on David Crockers Blog. In the photo it is shown the doubling up of wires at the thermistor but it does not describe the hookup at the Daughter Board. Do I take out the jumpers and install the additional wires into slot 1 and 4 or leave the jumpers in?

I have switched to the 2nd channel on the daughter board and now the temperature is much lower to the point where I must have the heat set at a minimum of 250 to extrude PLA, I suppose this points to interference from only having two wires. What do you think?