You guys might be onto something there. I found a different solution, that has worked for now. For some reason when using the dedicated save button things seem to work just fine. But as soon as we go though the save function in the top menu things go south.
I can tell already by the file size. Once saved in Separation Studio, depending which save function I have used, the file is 279 MB. Saved with the "save"button the file will be around 170MB and opens at the correct size in illustrator.