Sintron Kossel Z height will not lower print head enough

I have had this printer for a long while, it has printed perfectly from the day I set it up correctly. Last week the hotend started unscrewing itself from the cooling block mid print, this allowed melted filament into the top end of the threads, and no amount of playing around with it would let me get the filament out of the threads.

I had an almost new E3D sat here so I installed that. Filament flows through it perfectly.

As the E3D is a different length to the Sintron hotend, I obviously needed to reset the Z height. This is where I have hit a problem that is mystifying me, I cannot get the nozzle to lower enough to print at the required height, eg paper height.

I have done the following

Manually measured the nozzle height at home.
Around 240
Set it to 250 in Marlin.

Then in Pronterface:
M555 Z0 - resets Z
G28 - Home.
M114 = 250
G0 Z20 to drop the printhead down.
Dropped it further using Pronterface to paper height.
M114 = Z15.5
M555 Z15.5 to set Z height.
M500 to save to Eeprom.

Back to Marlin:
Changed 250 to 234.50.
Save.
Upload.

Test print and the print head is around 5-10mm above the print bed.

Tried changing the Z value via the LCD but it does not seem to have any effect.

It's been a long while since I originally set this printer up, I am missing something obvious. but I cannot figure out what the heck it is.

Edited 1 time(s). Last edit at 07/16/2017 05:39PM by Wibbles.

If you've got EEPROM enabled, it's probably using the old value.

Try sending M502 followed by M500 in the console.

Going from bad to worse.

I noticed that as I had fitted an E3D the levelling probe was too long, so I have shortened that. Hoped it would solve the problem but no...

The nozzle is now hitting the glass no matter what I do, I have tried everything that I know.

Switch printer on.
Hook up USB
Run Pronterface
G28 home
M114 gets me the print height, depending on what it is set to in Marlin. 237.40
G0 Z20
Drops the nozzle down.
Lower it to paper thickness
M114 gets me the Z value, -0.20

In Pronterface:
I have tried M555 z-0.20
I have tried M555 z 0.20

In Marlin:
I have tried Marlin 237.60
I have tried Marlin 237.20

I have tried:
M555 z0 before getting the Z values in Pronterface
M500 then M502 then M555 z0.20 in Pronterface to save the values

But:
The LCD still shows the old z of 5.30
I cannot adjust the LCD z below 0.50
If I adjust it to 0.50 and save it, it has no effect, the nozzle still hits the bed?

If I use Pronterface:
G28 Home
G0 z1
The nozzle drops to the paper height above the print bed, which is what I would expect.

I am doing something wrong when saving the z height to Marlin, but I haven't got a clue what it is???