Any layer masks? What about layer blend modes? Are the problem layers clipped to other layers? The latter could well give that effect.
Alt click the problem layer icon so you are viewing it in isolation. Set the Layer panel thumbnail to Large in the panel options, so you can see if the layer content is complete in the thumbnail.
Do a screen grab of the layers panel with all groups expanded, and upload it to this forum at full resolution.
I have occasionally encountered a situation where a layer, or group of layers defies all attempts to work out why it is not working as you'd expect, but duplicating those layers, or even ALL of a document's layers to a new document fixes it.
Good luck.