Layers Turning Off When Saving Artboards

I am running into an unusual problem with my layers.

I work for a print production company. We have to make proofs with multiple artboards. To make our print production files, we save out each individual artboard as it's own file (This is a feature that can be checkmarked when you hit "save as"). So, basically I turn the visability off on all the layers with my proof template, and I keep the artwork layer visable. This normally works just fine. I get an indivual file from each artboard and everything looks good.

Today, I have been doing that, and noticed that my individual artboard files are changing. When I open one of the indiviual files that saved out from my artboards, my artwork layer's visability is turned off.  That is not how I saved the file. I re-checked this many times to see if I was accidentally turing the visability off on that artwork layer. It is definitely not me. I keep my art layer turn on, I save out the artboards individually, and then the art layer is turned off when I open one of those individual files.

Has anyone else run into this issue?