This problem occured to me when I started using Skype. I merged the Skype contacts to the existing contacts (as they showed up seperately), a few days later I got the SMS bug. I re-flashed the phone, didn't merge Skype & phone contacts, and it hasn't occured for 6 months now.

Can anyone confirm the bug without using skype or merging contact information?

I also have tried the beta Nokia Suite, but sadly got an unspecified error message when trying to back up the messages to n9. It's true that the sms show up correctly in NSuite while being mixed in n9.