In the case of BuildingSkin, this plugin uses the hook OnStructureUpgrade, so every time a building block is updated, this hook is executed, which can change the grade and the building skin.
Please, I ask you for the complete list of plugins privately, as well as the other person. This will allow me to compare and see the plugins that affect the construction. This way, if another user has the same problem, I will also ask them for the list of plugins and I will be able to determine which are the conflicting plugins that may be causing this problem.
Once I have located the conflicting plugins, I will be able to contact the developers of said plugins to try to achieve a bypass so that they do not affect the changes that BetterTC makes.
I understand that it is frustrating not knowing what is happening and that it means spending time fixing this problem for the players. But the exact reason must be found and I am afraid that something is interfering in the process.