Could you clarify? You have two trees in FTM and two trees on the website? You have two trees in FTM and one on the website? You have two on the website and one in FTM?
The only way I can see that you could have two and both be syncing is two in each place but wanted to clarify.
How it happened is unclear; starting a sync process from scratch will give you a duplicate tree in one place or another.. but usually only ONE of them syncs.