I recall that back in the world of $work I could never get keys generated with PuTTyGen to connect via SSH/SFTP to the Linux/Unix servers I was supporting
Odd, I've been using puttygen-generated keys to connect from at least Win7 and now Win10 to a variety of linux systems since at least 2013 ... and probably even before that; that's just the date of the oldest key I still have a record for; I may have even started on XP (I'm not sure, but I held out on XP for a long time before going to Win7). My current key is RSA key, using 4096 bits.
Unlike Aldebaran, I don't hardlink to the key; I have used pageant (or a pageant-compatible key agent plugin in my password manager), and that works just fine. But I cannot imagine that putty has difficulty with files but not with a third-party pageant-clone.
Like hippo, I think this doesn't have so much to do with perl (yet)... though since the next step after getting the keypairs working will be to try to connect using perl, and we'll probably be asked to help with that after this is working, it's a good starting point to have confirmation that Aldebaran can connect using putty directly... and then support of the perl connection can continue in the same thread. :-)