We have also seen that issue on numerous occasions with different users. Sometimes the data moves to the bogus folders and then back again and all you need to do is delete the new duplicate folders. But sometimes the good data is in the new duplicate folders and you could delete that folder but not the other one as the delete option is greyed out, because it is the active default folder. So we move the data from the duplicate contacts, calendar, etc to the "greyed" folder, and then delete the empty one.
We've noticed two things. It happens when either the user has a new machine imaged, their current machine is rebuilt, or they log into a different machine, usually simultaneously. We cannot repeat it on demand, it's just one of those conditions always precipitates the issue. it may be related to mobile devices also, as it seems like everyone affected has either a Blackberry, iPhone on Good Messaging, or an active sync device, but as about 50% of user have mobile devices, that is hard to say it is actually a contributing cause. Users run the gamut across any one of 10 Exchange 2007 mailbox servers with each one having 11 data stores, so we sincerely doubt it has anything to do with database corruption as a few posts about this problem speculate.
Users are in cached mode using OST's but if you look at their mailbox in non cached mode, you see the same duplicate structure in Exchange.