The linux box seems fine -- I can use my ubuntu workstation and connect using ssh from the command line just fine:
ssh -i /path/to/file.pem email@example.com
The question is I think more about puttygen than anything else. What is wrong with the file such that puttygen cannot import it and convert it to ppk format? Is it that each line is terminated \r\n rather than just \n?
Alternatively, might there be some way to convert the pem file to PPK using my linux workstation?