What were your export settings? If you didn't use PDF/X4, try that.
I dont know if you have the same issue but i had this happen to me a few times. in my case it was because there was RGB artwork In my CMYKfile. We changed it from RGB to CMYK and it worked.
I'm assuming your overlay colours are spot colours (be they Pantone or whatever). Check your setting in Acrobat, re: Output Preview > Simulate Overprinting. If it's not checked, that will totally affect how it appears, and will cause exactly the issue you are experiencing with your overlay colours. If you don't need spot colours in your file for print, I suggest you convert them to process for the purpose of digital editions. The quickest and easiest way to do this is to go to your Colour Swatches > Ink Manager > and check All Spots to Process