I'm having the same/a similar issue, and am wondering whether 1) if you were able to do the photo sync settings fix, did the situation *stay* fixed, and 2) whether anyone has found any other solutions. I have iPhone 4, iOS 5, iTunes 10.5.2.11. I'm not sure if this problem started after a particular iTunes update. While it never happened before I installed iOS 5, I don't think the start of the problem coincided with that particular change, but rather some time after. I'm running Windows 7.
Basically, as others have described, after syncing my iPhone if I click on another tab in iTunes (e.g. the "Music" tab for my library), I get the dialogue box that says that I have changed the settings on this iPhone and it gives me the option to "Apply" or "Don't Apply." Except that I haven't changed any settings. I hadn't done anything unusual with my phone prior to when this behavior seemingly randomly started. I haven't changed any settings, moved my library (as another poster - either in this thread or a related one - reported having done), etc. I tried the fix of changing my photo syncing (although I was already syncing a particular folder of photos from my Windows 7 laptop, with no issues, for some time before this started happening, so IIRC I turned syncing of photos off and then back on). I tried the "reset warnings" fix I found in another thread ("I have managed to fix it by first clicking the Apply button then right-clicking on the iPhone in the Devices list in iTunes and selecting Reset Warnings from the context menu."). The next few times I synced after doing those things, everything was fine, but not that long after that, the issue came back.
Strangely, the only thing that maybe seems to correlate with this "you have changed the settings" message is that I seem to see it if, after I sync, while my phone is still selected, I go to the apps tab for my phone. The iTunes screen that shows the arrangement of all of my apps on my phone loads, and then when I go to click on something else it's as if iTunes thinks that I just told it to sync apps or something, as I get the changed settings dialogue. I *do* sync apps, but again, I've been doing so since I got the phone, and none of times I've gotten that message have I actually changed those settings. I should also note that this issue doesn't happen *every* time I sync, and I have no clear sense of a pattern of when it does vs. when it doesn't.
So...people who changed photo syncing or reset warnings, has the problem gone away completely? Anyone else find any other fix?