@me PuTTY is #freesoftware so one way to go would be to build it yourself from source, then add some extra debugging output in the part of the code where it is looking for public keys. Then you will find out what happens.

The source code seems to be available here https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html and here https://git.tartarus.org/?p=simon/putty.git

Good luck! 🙂