cgi-bin files would have been left over from ubb classic not threads which used perl not php.
Guessing on what you have.
I would need to see a sample of some file names to know for sure.
But anyway ubbthreads is almost all files ending in .php and would not be normally installed in the cgi-bin folder.
Classic was most all .cgi and .pl files and would have been installed in the cgi-bin folder.