This bug has been added to the tracker:
https://winscp.net/tracker/786
https://winscp.net/tracker/786
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On v5.0.4 I'm still seeing this issue.
I've a mix of password sessions and saved keys but regardless everytime I initiate a transfer, I still get the problem.
Additionally on 5.0.4 I still get the Invalid Access to memory error on start up.
I'm using 5.0.4 and having this problem. Note that I am NOT using keys or passphrases but simple password authentication.
I have the "Remember password of main session for background transfers" checked, but the first time I transfer a file after opening a session I get prompted for the password again.
This is definitely changed behavior from the 4.x versions I was previously using.
I get the Invalid Access to Memory bug and the behaviour I notice is that it resets my local directory back to the installation directory. Hope this helps.