Unfortunately the two inner layer pads do not render when there is a zone connection regardless of the remove_unused_layers setting, This is a problem with the way the zones calculate the fill around a pad (clearance) and hole (hole_clearance), I have found that the resulting clearance around a THT pad connected to the zone on an inner layer is the greater of the clearance and hole_clearance. So, this constrains the size of the copper pad to be greater than the hole_size plus the hole_clearance * 2. So, a hole size of 0.3mm with a clearance of 0.2mm requires the pad to be at least 0.7mm to cover the clearance and should likely be slightly larger so that you do not create a seam at the intersection.
I wonder if it is a download issue? I posted two zip files with the same name. I think I should have appended the second upload with a version number or something to make it obviously different. I don’t know how this forum handles duplicate names. I changed the name by adding “v2” at the end and uploaded it here again.
nettie test.zip (21.2 KB)
EDIT: Well that is weird. I changed the name but I see it uploaded with the same file name as before. Maybe the forum compares to the other uploads and if it is a duplicate ignores it?
Another thought. What version of KiCad are you using? I used a couple different shapes to help me debug how the zones are being generated. I wonder if the “cloverleaf” is a result of the corners of a “rounded rectangle” of the smaller inner rectangle?
The cloverleaf is because @BobZ is using the fallback graphics mode rather than accelerated graphics, I think. (In fallback graphics, color blending is not well-supported, so you get artifacts where different shapes overlap. Rounded rectangles are drawn as 4 lines with rounded ends, overlapping in the corners, so the overlapping corners are brighter than the non-overlapping edge parts).
It seems you are correct although I do not remember setting fallback graphics. I wonder if that might be the default for some reason. My laptop seems to work OK with accelerated graphics and that cloverleaf is no longer visible.
I think that is asking for trouble in many circumstances. I usually think of e-mail attachments. You are never sure which you are viewing.
Anyway my responses here reflect a philosophy which I have been trying to keep. That is:
Just because I respond to a thread does not mean that I have all of the answers. I think that very often the original poster leaves open questions which are obvious to all but the original poster. So even if I cannot go much further than asking those questions I think I am likely to be helping the resolution.
In this particular case, the discussion got into some matters outside of what I know about KiCad. I appreciate that KiCad is open source, and there have been a few situations where I have managed to use a text editor to solve a problem. This although I thing I am not very skilled in coding or programming. That is what I did for the internal layer net tie, and I remember fixing another problem on a pcb design where some footprint somehow ended up a looooooooooooooooooooooong way outside of the normal field of view.