Having an issue since the latest update with my files not actuall saving the colors.

[MMP Production]

Running on Windows:
Since the update I keep getting really weird results when saving some of my artwork, like lines in the images or it completely not saving the color info at all. I am a printer, and sometimes the images look fine on the screen, but when I got to print them, the colors completely disappear.
I am now having to do some fancy footwork where I have to create a new file, place the file, go to Object and then I have to Flatten Transparency. And then I have to save it as a PDF X1a file.
Last week to get around this all I had to do was save a copy as a PDF X1a file. As of this morning that didn't work anymore. I am losing my mind, can anyone help so I can just save my files like I have been doing normally for the past decade?

[c.pfaffenbichler]

Could you please set the Status Bar (lower left) to »Document Color Profile« and post screenshots including the pertinent Panels to illustrate the issue? 

What are the Edit > Color Settings?