When I use my skin, the left leg's pants don't render even if the left pants leg is on, and I did texture my skin right.
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Additional note: I'm not really sure if this is a bug. Maybe it's not intended. I could image Mojang wrote some code that splits the skin into multiple parts and then tries to figure out if the skin is transparent instead of checking the whole file, because they don't want to render players with black or white (instead of transparent) background covered in a solid overlay - which makes sense, but the implementation might be faulty here.
In case it is intended to work the way it does, I would love to hear the reasoning for that because I can't make any sense of it.
Either way, it's very confusing and definitely not obvious how it works.
Before this is marked as a duplicate: It's not a duplicate of MC-45213, where users just failed to fill out the right parts of the skin.
This is thanks to the weird way Minecraft decides when to render parts of the overlay.
I was doing some research on this for an avatar rendering project, you can read the full thing here, but long story short is that some parts of the overlay don't render when a certain area that contains that part has no transparent pixel in it. This probably sounds confusing, so here's a map:
[media]On the left side is a common 'skin map', where each part labelled with '2' is an overlay part. The right side shows the areas in which Minecraft searches for transparent pixels. If one of these areas is completely filled with opaque pixels, the overlay part that's contained in that area will not render.
In your case, the bottom left area (lightblue) is filled and thus the left leg's overlay ('LL2') is not rendered.
Make sure your skin file is only filled where it has to.
[media]When you put the 'skin map' over your skin file you can clearly see the unnecessary parts (in LL2 and LA2) that should be removed:
FYI: This bug was driving me nuts and I literally spent days trying to figure the hell out of it. TML!