Thanks for sharing your solution.

Ok, for me the problem turned out to be files over 100KB.

I had to turn ResumeSupport off in my transfer options to get passed it.

I am having the same issue. Doesn't happen all the time.
But the files it happens to, it is consistent.
my file is a text file. I've opened it in text pad, resaved it and retried with same error.
Unfortunately I don't have access to the server side logs.

Any ideas what could cause this?

I am on version 5.9.2 as well

I there any information about the problem in your SFTP server log file?

I have an automated process and sometimes (not all of the time) I am getting an error:

2016-10-19 08:41:34.812 Error message from server: Bad message")
< 2016-10-19 08:41:34.843 Script: Cannot close remote file 'HF1018.asap'.
< 2016-10-19 08:41:34.858 Script: Bad message (badly formatted packet or protocol incompatibility).
< 2016-10-19 08:41:34.858 Error code: 5

Wondering if anyone has any ideas on how to avoid this.

Using WINSCP Version 5.9.2 on windows 7 using SFTP transfer protocol.