Kicad 5.1.4 solder mask issue

I am quite new to pcb manufacture and kicad and am having an issue with the solder mask layers. I am using kicad (5.1.4)-1 64-bit windows version.

I have created a pcb which I have engaged PCBway to manufacture for me. However, after generating the gerbers and submitting the files to them they have come back stating that there is an issue with the solder mask.

Failed reason:

Soldermask layer is wrong ,pls cancel the option"Negative Polarity"for soldermask layer when exporing the gerber files from Eagle software.;

I checked my settings and the negative polarity option is not selected - in fact it is grayed out and not selectable (see below image).I have had a look at the gerber files for the solder mask (see below) and it looks like the mask covers the entire board including the locations where the solder paste would be applied. I would expect that the solder mask should not cover the solder paste because otherwise the solder would not stick at these locations (unless I completely do not understand). And I am assuming this is the issue so I have deleted and regenerated the gerbers but keep having the same issue.

My board setup design rules for the mask are:
Soldermask clearance: 0.051
Solder mask min width: 0.25
Solder paste clearance: -0
Solder paster ratio clearance: -0.000000

Snips of solder paste and mask layer

Gerber export settings

Does anyone know what the issue is? or have any suggestions for me?

Edit: It looks like there is two solder mask layers overlaid when inspecting the gerbers (There is only one in pcbnew)


You can read this FAQ article: How does solder mask layer work?. You can also give a link to your project (not just gerbers) here, it may be easy to find the problem by inspecting it.

You probably have some graphic shape drawn on the mask layer.

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