Issue with duplicate layers when importing Illustrator files.

Explanation:

When I create a master logo file in Illustrator, I structure it so different orientations are on different artboard, ie landscape, portrait, compact etc. Then I will have the various colour options for each orientation on different layers ie, colour, reversed, white, black etc. This way I only have one file for all the different formats available.
Then when I use them I import the artboard with the orientation I want and switch on/off the appropriate layers to chosen colour variation I want.

Issue:

Previously when I would import Illustrator files, I would only see one set of layers regardless of how many artboards were used in the Illustrator file. But over the past month or so, when I follow this same process i've been using for a years of importing the Illustrator files in to InDesign, i'm now seeing the layers repeated for each of the artboards.

Simple example to help illustrate. If I have an illustrator file with with two artboards and two layers called 1 and 2. Normally when I import this, I would be able to choose the artboard I want, then select between the two layers, regardless of which board select. But now im seeing FOUR layers. The two layers dupllicated for each of the artboards which means the layers i'm now seeing are 1, 2, 1, 2.

When:

Not entirely certain but I think it started over the past month or two. I didn't think too much about it at first.

This might seem like a minor inconvenience and is significantly affecting my workflow If I have multiple artboards with multiple layers, it's actually really difficuly choosing the layers I need to switch on/off.

Has anyone else experienced this? Is this a function that has simple been changed? Or is it actually a bug.