The only way we were able to fix it was saving the file as a png in Photoshop and then placing it in InDesign
PNGs have to be RGB (or Grayscale), but InDesign doesn't honor a PNG's color profile—the Indesign document's RGB profile gets assigned. So the reason PNG worked is probably because the profile got stripped. You could confirm that by saving the logo in another format and don't include the profile.
A sidebar question I did have was that under edit - color settings - color management policies, under rgb it is listed as preserve embedded profiles. I am wondering if I had that set to "convert to working space" if it would have helped.
No, convert to profile only converts native InDesign colors—it has no effect on placed images.