Could be a transparency blending space mismatch, perhaps....
I'm working on a document that is set in CMYK...
but how is this possible when it's the images on the Master page that is being altered, and it's random!
InDesign doesn't have a document color space—you can mix CMYK, RGB, or Lab colors and images on the same page.
The image on your master page could be an out-of-gamut RGB image. If you make pages from the master and add any transparent object to one of the pages the image would be displayed in the document's Transparency Blend Space. If the blend space is CMYK an RGB master image would display as document CMYK, but only on a page with transparency.
When you select the image on the master what Color Space and ICC Profile show in the Links panel?
Ok, I double checked a lot of things and here is all the info:
The vector file that I am using on the Master page (as a footer graphic) is RGB.
All of the pages have some element overlaying it, some pages only have a text box that drops down to partially cover it (not the color part, a white area), and some have an image. But there is no consistency with this information as it literally just seems to be random pages. If it were text boxes causing the issue, wouldn't it affect all the pages that have text boxes touching this region?
The Transparency blend is set to RGB.
Here are some screenshots.
Here is page 9 how it looks in InDesign showing all of the element box lines:
And page 9 how it looks in the PDF:
Now, here is page 14 in InDesign:
And page 14 in the PDF:
Thanks for your help Rob and Peter!
So it looks like the shift is happening in the exported PDF not the ID layout. What are your export settings? Try PDF/X-4
Looks like your colors are out of the CMYK gamut so if you plan on sending this to a press the color will eventually be converted.