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When running in a terminal and requesting a pty on the server, the Unix port of Plink turns off OPOST. It does this to ensure that if an application on the server turns off OPOST in its pty and sends a bare LF, that will make it all the way to Plink's terminal. This, though, causes the problem that if Plink's stderr goes to the same terminal as its stout (the usual situation), Plink's own messages, sent to stderr, won't get their '\n's translated to CRLF. The fix for this is to turn on OPOST around any internally-generated writes to stderr. This is easier said than done since there are many writes to stderr in uxcons.c, and at least one in logging.c. In addition, the writes from (e.g.) ssh.c of application data should probably not be affected.
Audit trail for this bug.