no no, it's iTunes and only with some calendars some duplicated and some tripled:
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if I uncheck one both appear unchecked after syncing and vice versa
I see the problem... If your iOS device already logs into MobileMe, there's no need to sync anything related to MobileMe via iTunes. your iOS device will synchronized directly with MobileMe over the internet.
Otherwise, you'll get duplicated entries from:
- MobileMe Calendars (directly accessed)
- MobileMe Calendars (synchronized via iTunes)
You should disable calendar sync via iTunes, and most likely do the same for Contacts and email