I have heard 100 problems on this forum and this one seems new. At first I thought maybe temperature but you said "different PLA filaments" and *most* PLA colors are not temperature sensitive (a few are).
So I don't think it's temperature. Also you said it seems to happen 5mm off the bed every time. This makes me think it is related to the Z height. Maybe your screw threads aren't equal. Or maybe the Z axis gets stuck a little. This kind of thing happens a lot. So maybe the "darker" layers are closer together than normal (over extruded) or maybe they are farther apart (under extruded). Either could cause the layers to be darker.
Could you post pictures of other objects? Does this only happen on transparent colors?
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IRobertI 521
That's weird. Does it really happen with any PLA? I'm thinking that it could be the infill showing through on slightly translucent plastic. Do you have a picture of a more plain object, like a box? I think that would help in diagnosing what's happening.
To rule out wild temperature fluctuations you could watch the temperature during the print and see if it remains stable. Both cura and Pronterface can give you a temperature graph if you use them to print if you don't want to stare at the ulticontroller during the print.
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