These problems I am having are totally putting me off from using FTA.
I have not been following parts of this discussion in detail because much of it is of no particular relevance to me. However, I suggest that there is no reason to stop using FTA as any problems that you are experiencing will not have been introduced by FTA and there is much benefit to be obtained from use of FTA in other areas. The most likely source of your problems are . . .
1. FTM
2. Ancestry
3. the data entered to the above two programs.
1. I do not use FTM so cannot offer any suggestions. I don't even understand some of what you and others have posted previously.
2. I only keep a direct-ancestors-only tree at Ancestry in order to assist with matches to DNA cousins. However, when I look at other trees having received hints concerning possible ancestors, I often find that the associated trees are a complete mess with many individuals duplicated and varying data associated. I don't know whether that is due to mistaken input of data or a mess-up within the program. I do not notify the tree owner as I assume that they will see the mess and try to do something about it themselves. I prefer not to put myself forward as the messenger to be used for target practice.
3. I do not wish to make any suggestion that you may have caused any problem by entering incorrect and conflicting data but if I was in your position then I would make multiple checks of my data entered (not just the values), assuming that I had confused the program with my input, just to make sure that I had not overlooked something. If the error(s) persist then I would change/remove data in an effort to get rid of the error(s) and then re-insert the information one item at a time, checking the effect at each stage. It may be a very slow process but it should identify whether I had caused the misunderstanding or the program is not handling the data correctly. If the program is at fault then DO contact the developer or provider with a suitable description of what happens in the simplest possible terms so that the occurrence can be easily reproduced by them.
If you need further assistance from forum members then it may be helpful to create a simple situation with only a few individuals in the tree, which others can then try out for themselves.
I hope this helps. Good luck for a speedy resolution.