In the latest development release I have fixed the bug that textures in the 3D building generation have to be square in size. But while making this fix I also broke the backwards compatibility of old BTC files partly. So prevent such issues in the future I have added a new file format that has less backwards compatibility issues, this new format is called BT2.
For now the Building Texture Configuration Editor can read both formats, so you can convert your old configurations by loading them in the editor and then saving them in the new format. I have also made a command line conversion tool that you can use: btc_to_bt2.