@Enchantedprey - make sure that you're persistent and patient, even if the support person doesn't seem to grasp the problem. I'm not sure that the online chat guy (who was super friendly, BTW) ever actually understood exactly what my issue was, because although he said he could see the items weren't marked as owned, he seemed to think that as long as I could use them in game then everything was okay. Whenever he asked if my problem was solved I just kept saying no, and reiterating that the issue was individual items not showing as owned in the store so they didn't count towards CYS (I think I must have typed that about ten times!)
Eventually he said he'd have to escalate, and a couple of days later I got an email saying they'd fixed the problem, without anyone else contacting me, so I assume whoever it was escalated to could read the transcript of the chat. Don't give up, and hopefully they'll be able to fix it!
