Have you checked that this PDF on another machine to see if the photo issue is not just on your computer?
For the animations/transitions problem, see page 18 of the Presenter manual: http://help.adobe.com/en_US/Presenter/7.0/presenter7.0_user_guide.pdf
Yes, I've checked that it's not just my computer. In fact, I've called Adobe about this and multiple other issues. After putting me on hold for hours at a time, they've told me they "have escalated" my issues and that they will call me back once they find a solution.
In my experience, they have never called back. Meanwhile, I have found time-consuming work-arounds for every problem they couldn't solve. I will seriously discourage any company or individual I work with from buying any Adobe product. Their customer service is on par with Sallie Mae, and as anybody with student loans can tell you, that's just really awful.
Okay, so I re-read your original post and believe I misunderstood your problem.
"In PowerPoint, everything works fine when I play a slideshow - my animations show up, all my photos are there, everything's peachy.
When I publish a pdf using Adobe Presenter, suddenly my photos do not show up in the slides. However, if I go to Thumb view on the sidebar in the pdf, I can see the photos on the thumbnail slides. So why are they not showing up in the actual slides in the pdf? All the text, etc. shows up, although our logo at the bottom of the page also fails to show up in the pdf slides, although I can see it in the thumbnail slides in the pdf."
1. Do you mean that the photos tied to your animations/transitions aren't showing up?
2. Are other photos on static (non-animated) slides showing up?
I apologize for not responding in a timely manner, but Adobe spent weeks on this and eventually got back to me to tell me that the only solution was a time-consuming work-around they had told me about weeks earlier. Presenter continues to have all kinds of "quirks" that require tons of time, their hold times are still horrible, their support people on the phone are difficult to understand, and often can't even get me answers.
FYI, they were photos in static slides, no animation. This happened with every slide in the presentation. The work-around that Adobe figured out (then took weeks to attempt to trouble-shoot only to get back to me with the same work-around) involved importing the photos, saving them to another folder, deleting them, and re-importing them. Because of another Presenter quirk, I had to import the photos, crop them, save them to another folder, delete them, re-import them from that folder, and crop them further.