The % indeed has to be encoded as %25 for the session URL. And this has not changed since 5.9.4.

Enable password logging
https://winscp.net/eng/docs/ui_pref_logging
and check the log to see, what is the actual password that the old version is using.

Also you can export the settings and transfer it to your new machine.
https://winscp.net/eng/docs/config#transfer

If you still have a problem, please attach log files both from the old and the new machine.

I just downloaded and installed WinSCP-5.11.2 on my new Windows 10 computer. I am attempting to connect with multiple sites. Two of the sites use the percent sign as part of the password. I can not get them to connect and when I generate the Session URL/Code it shows "%25" instead of "%" in my password. Another site that does not use a percent in the password connects fine.

My old Windows 7 computer that is running WinSCP 5.9.4 is able to connect to the sites without a problem and the Session URL/Code shows the password correctly.

How do I get WinSCP 5.11.2 to connect when the password contains a percent sign?