No mods on my iPhone. I have the latest version of iTunes and the 1.0.1 version of iPhone software that I had hoped would fix this problem. I just kind of assumed everyone had to restart their iPhone in order for iTunes to sync.
i did uncheck "automatically sync when iPhone is Connected" but I didn't think that meant that the little iPhone icon won't show up in iTunes unless you restart. Anyone else have this problem with "automatically sync with iPhone" unchecked?