Oh right, this is happening with Photoshop and Illustrator, which is why is didn't post on an individual programs forums. I forgot to add that to my previous post. Do you recommend that I post in both the Photoshop and Illustrator sections?
Edit: I did more tests. If I use the branded color 0039a6 in Illustrator and save it out as a png, tga, jpeg, pdf, and I then open one of those exported files in Photoshop, the hex value has changed.
If I use the branded color in Photoshop, exporting a png keeps the color as the correct hex value. JPG doesn't, which makes sense due to compression. So now the question is, why are the files I'm exporting from Illustrator and opening in Photoshop showing different hex values. You would assume that the pngs should be okay from both Photoshop and Illustrator?