This is the first time I've read about this problem. Something has either gone wrong with FTM or this is user error. At any rate, if you're uploading a "linked" tree from FTM to Ancestry.com, you should not have a "new" tree in FTM, only a new one at Ancestry.com.
Provide us with a little more detail on what you've done--and a link to your tree at Ancestry.com. We'll get this sorted out for you.