@paulinefrommarraween,
I am a bit confused about the sequence of events. I suspect my confusion stems from the phrase, "once the device was totally devoid of added things". I think that making changes to the things being synced, e.g., checking an event in Photos, or unchecking an album in Music -- or, unchecking "every check" -- has no effect until you click Apply or Sync. So, you simply unchecked "every check" and click Apply or Sync, right? Whether the unchecked stuff really disappeared from the iOS device before you clicked Apply or Sync, you don't really know, do you? Or did you examine the iOS device directly immediately after unchecking?
Then, what about unchecking "every check"? For example, in the Photos tab for my iPhone 4S I have checked "Sync Photos from iPhoto", selected the radio button "Selected albums, Events, and Faces, and automatically include the 10 most recent Events" and, under Events, I have checked some events in addition to the 10 most recent, which are checked but greyed out. If I uncheck "Sync Photos from iPhoto", then everything else that was selected or checked is greyed out, so I cannot unselect or uncheck them. Would/did you in such cases, (A) merely unselect or uncheck, say, the events, or (B) (A) plus then uncheck "Sync Photos from iPhoto", or (C) just uncheck "Sync Photos from iPhoto"? It would seem sufficient to just uncheck "Sync Photos from iPhoto", but you never know.
Regards,
Richard