This issue is being tracked already:
Issue 2259 – Badly encoded SFTP packet when renaming a file using SFTP version 5 and newer

Downgrading to 6.1 or older should help.
Fixed version will be released shortly.

I'm sending you an email with a development version of WinSCP to the address you have used to register on this forum.

I believe I am uploading to a Windows server.

Every upload returns:

Bad message (badly formatted packet or protocol incompatibility).
Error code: 5
Error message from server (en): Badly formatted SFTP packet

I tried dropping back to SFTP version 5, no luck.