I would love to take a look at what you are experiencing, I have personally not ran into this, but if you can attach a couple small subsets of the two files. I can attempt to append them on my end and see what happens or if I find something glaring wrong that could be causing the issue.
In the meantime, here are some resources about adding data that might assist with this issue.
One thing to check is that both column names and column types must match.
Also, when you mention [Column Name] - do you actually get the same column name mentioned twice or you get it for two different columns?