Aaron, I was wondering if you have solved this. I have noticed this issue for some time now (over a year). I just upgraded to AP 3.5.1 and was hoping the problem was solved. I don't think your jpeg theory is key, because I observe the 'problem' with both raw and jpeg.
Here is another head scratcher. I have a project with 110 items in it, mostly raws from my 7d. Some are psd's from Photoshop. One of the psd's does the automatic switching. None of the others do it. I also found that one of my raws does the auto switching. These shots were all from a photoshoot I did in a single day with the same camera. They are all referenced files, and I see no other distinction that makes 2 of them 'work' and 108 of them not!
The above test was done on my iMac.
The following test, I did on my MBA. I found a project where all 101 images/movies were taken with my G15. In this case, all the movie files did the auto switch. None of the jpegs did the switch (except 1, hmm...) and almost all the CR2 raw files caused the switch, except a few.
So, I really don't think this is an issue based on a single type of Mac, or a corrupt preferences file. I've even tried to repair/rebuild the database with no changes. And, I think most AP users, like Phosgraphis, discover that all their images don't cause the auto switch, even 'tho they thought they did. So this may be a bug in AP that Apple hasn't yet discovered.
I'm with you...this is a time-saving feature, when it works. It would also be VERY nice if it would snap back to the Adjustments panel after you dropped your image(s) into the Library.