Unwrapped objects before joining them together - now the UV looks weird

Some of the meshes are intended to be overlapping (copies), but once i open the UV png in photoshop i see like if most of them would be overlapping (multiple copies). On images below is the screenshot with marked meshes that are supposed to be overlapping / copies. The others are single uv mapped meshes. I have no idea why they show on png as less transparent than the one in the corner on the top-left.


Any explanation and advices are appreciated.
Thanks.

Ok I think I have found the culprit. Another copy of the material appeared in materials when i joined them all together. After removing the extra material copy, they are all equally transparent now (i was expecting the copies to be less transparent on png tho, but i can live with it).