What "cli"? Are you using winscp.com or winscp.exe /console? WinSCP does not handle the clipboard anyhow in the console. It's the console "manager" that does. What console is that? cmd.exe? Windows Terminal?

There is a small bug in how copy-paste happens in cli ,
When you do Ctrl-A and select whatever is there, Ctrl-V doesn't always pastes but deselects it, but second try always works. I home it's not my old keyboard but actually a bug.