Ok, I've run across an odd one that I can duplicate on my system easily (Windows 7 w/ SW2016). This started happening 2 or 3 months ago so I suspected it was a display driver issue but updating the drivers to the latest version didn't have any affect so I don't believe that's the problem
If I add a new configuration to the subassembly (new configurations, derived configurations, or exploded views), or add / delete a component in the subassembly all componenets and subassemblies in the parent assembly change to the Default Shading Color (Document Properties / Model Display / Shading) in the parent assembly. If I look at the Appearance History in the parent assembly nothing has been added. If I save, close, and reopen everything is back to the original colors.
Here's an example. The first image is the parent assembly.
The red parts are a subassembly (all subassembly parts have had their colors individually set in the parent assembly). I opened the Red subassembly (right clicked on it and open it). I added a new configuration but didn't do anything else. Saved and closed the sub-assembly and this is what I see when Solid Works goes back to the parent assembly:
I know all the parts are switching to the parent Default Shading Color because at this point I can go into the parent assembly properties and change this property and everything changes to the new color.
Again, if I save, close and reopen everything goes back to the original image colors.