Well, the debugging output shows something is going wrong because commands are being pipelined but then responses are arriving late anyway... it makes me think that the problem is not in the module but in plink, in Windows or in the network.
Where is located the server? is it in the same LAN? data-center? city? country? continent?
What protocol are you using for the WinSCP tests, SCP or SFTP?
What Windows version are you using?
I will try to reproduce the problem myself tomorrow in a Windows machine.
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