This must be some weird edge case. Most people (including me) don’t use Finder’s native tabs and use just TotalFinder tabs. Those two should not interfere unless you have “Finder -> View -> Show Tab Bar” always shown. In that case you will see Finder’s native tab even if you have just one created.
Also please make sure that you have “Finder -> Preferences -> General -> Open foders in tabs instead of new windows” unchecked. This keeps TotalFinder behaviour from the times before native tabs were introduced.
You might always try to reset Finder and TotalFinder into factory defaults to see if the issue is in your plist config: