I have tried numerous times to recreate the keypairs, but it seems that after the first time, if I tried again, it seems to take forever, not sure if you want to call this a bug or what. I found out if I restarted my server, then it goes back through recreating a new set of keypairs, it takes maybe 5 minutes. So, to me it seems as if there is a problem with it running in memory for a long time, this is going through Kleopatra. If I do this through cmd line then is goes much faster. Or maybe you could shed some light as to why it does this, thank you.
The OS runs Windows 2008 R2 , on a Oracle's Virtualbox, so I wouldn't consider this being a headless Windows installation, why? When you first create your keypairs it goes pretty fast usually under 5 mins. But if you recreate or try an create a new keypair it never completes, takes 20+ minutes or longer. But if you shut down the OS, or restart the OS, and try it again then it completes in under 5 mins.