Layers - Paste not remembering layers when copying

I'm using AI CC2014. When trying to copy certain layers between files the layers are being "released" and I'm losing my layer structure. This behavior is unpredictable and seems to be limited to certain layers. Other layers can be pasted retaining their sub-layer structure. The "Paste Remembers Layers" option is active. Am I missing something obvious?

Monika,
Forgive me for being a bit lazy but I've closed my files down after we manually copied and pasted each sub layer from file to file to rebuild the structure. It's pretty straightforward though... I had a top layer with nested layers. When selecting all of the layers and copying them from one file to another the nested layers where released somewhat randomly. That is to say I didn't end up with a completely flat structure - some nested layers retained their structure and others released their artwork to the top layer. It didn't matter whether "paste remembers layers" was active or not. It didn't matter whether I used COMMAND V or COMMAND F.
When I tried to replicate the problem using a new file I could not and the behavior was as one would expect.
I verified the problem sending my problem files to an associate who experienced the same behavior. When we could not get the layer structure to copy we decided to rebuild the sub layers one at a time - copying the sub layers over one at a time.
I'm working with a team on a UI and we each "own" separate parts of the interface. We rely on the ability to merge our work into a "master file" on a daily basis. We each "own" certain layers and if we can't easily drop in our updated artwork (layers intact) it's pretty awful. I assumed I was doing something wrong until my associate had the same problem.
This seems like a bug and not user error unless I've changed some setting that I'm not aware of.

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Layers - Paste not remembering layers when copying

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