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I've had the same thing happen, lots of dupes. I have been syncing tasks to my Blackberry via Missing Sync. In particular, items in subgroups were always being duped and moved out of the hierarchy to the top level in each project. Also, as noted by Kurt, some weirdness with erratic context assignments among the duped items.

I toggled Missing Sync to overwrite the Blackberry tasks 100% of the time and that seems to have solved the problem. I can't enter or change tasks on the BB now, but hardly ever did, and always carry other ways of capturing to-do ideas anyway.