Good. I've improved this anyway:
Issue 2244 – Do not use directory listing to keep FTP session alive by default

Thanks for the quick reply. Turning off keepalives did fix the issue, but then I get logged out after a few minutes of inactivity. Better yet, I changed the protocol from FTP to SCP (not sure why I ever set it to FTP) and used null packets for keepalive. Now I have the best of both worlds. Thanks for helping me sort out my confusion.

I'll look into it.
Meanwhile, do you have to have the keepalives enabled at all? Cannot you just turn them off?
https://winscp.net/eng/docs/ui_login_connection

WinSCP seems to re-read directory contents about every 2 minutes. While WinSCP is retrieving the list, the UI is blocked and the program is unresponsive. When working in a directory with several thousand files, over a VPN, it can take almost a minute to get the list of files. That only leaves about a minute or so do to any work before the UI is blocked again. Sometimes actively working in WinSCP seems to delay the directory re-read, but still, every few minutes it becomes unresponsive as it reads the directory contents again. Is it possible to control the time between directory re-reads. It would be nice if the directory listing could be run in a background thread so that it does not block the UI.

P.S. I just noticed this in the log.

Could you use a different command to keep the session alive instead of a directory read? Maybe pwd?