I am launching SCP through Visual Studio, which is feeding the key information to SCP. I tried overwriting the file by uploading twice, which worked. Don't know why SCP is trying a different authentication when saving then when copying...
How is VS feeding key information to WinSCP?
WinSCP is run like:
"C:\Program Files (x86)\WinSCP\WinSCP.exe" scp://XXXXXX /privatekey="C:\Users\s.ostenberg\AppData\Local\Temp\tmp66F4.tmp"
I assume the temporary file disappears before you try to save the file.