Transparency showing gaps in faces that aren't there?

[matt0eden]

I'm pretty new to Maya, and i've looked around but didn't find an answer so im trying to post here,

I'm not really sure how to explain this, but I have some Custom script to change the transparency of my model to various levels and it's showing me something very strange with my model.

When the object isn't transparent the surface of the model is totally fine.

But when it is made transparent, some faces are missing, or more transparent than others.
this hasn't been an issue in the past and only started happening yesterday.

the code I am using is 

setAttr "standardSurface1.opacity" -type double3 0.9 0.9 0.9;
or

setAttr "lambert1.transparency" -type double3 0.1 0.1 0.1;

I have gone through Cleanup steps and there are no Ngons, non-manifold, holes, zero faces area, and they all have map area and geometry area. 

It's reminiscent of when half your faces get deleted at random for no reason, except those faces are still there, so im worried there might be some corruption or error somewhere that i have no idea how to fix.

And Ideas?

[Christoph_Schaedl]

Have you tried to render it? Or tried it in Marmoset?
Cause the Maya viewport ist the best with transparency.

[matt0eden]

Thanks for taking the time to respond.
using Arnold it seems the transparency looks fine there, so its just a bit concerning that some faces are effected more than other in the viewport.

not sure if it's helpful but if i were to delete one of these faces and replace it with a new one, it seems to fix the problem. And i could do that, but some of those are harder to see than others, not to mention the tedium