Sorry to hear that you are facing this issue. Can you please check layer options dialog?
From panel flyout open Layer Options and see if the thumnails for “Layers” “Groups” and “Objects” are selected and “Top Layer Only” is Not selected.
Also “Show Layers Only” check box should be deselected.
let me know if this solves your problem or not?
An error occurred while saving the commentCharles commented
I launched illustrator from an eps file and layers were not showing so I figured it might work better if I launch Illustrator on its own first, then open the file. I quit out of everything, relaunched Illustrator, then opened the file. After that, I had to click another tab in the same panel as layers then click back into the layers tab before it showed up again.