First off, thanks so much for sharing this process with the lot of us. (After enjoying this thread for over a year, that was long overdue.)
Second, I think your iPhone is, indeed, applying a filter to your photos. (You can see an example of them here.) When you've got your camera app open, look to the right of the shutter button (if you're holding the phone vertically) for the icon of three entwined circles. If you tap it, I believe the screen will show nine filtered versions of the view. Your pics look like they're getting the 'Process' filter. Select the center option to go back to shooting with no filter. Hope that helps.
edit- Oops. Hadn't refreshed before nroose posted.