You possibly missed the premise that the "Keeping remote directory up to date" function has to be started on already synchronized folders. Your claim that "Synchronize on start" uploads everything implies that the folders are not synchronized.
See https://winscp.net/eng/docs/task_keep_up_to_date#how_it_works

Or you have a general problem with the synchronization:
https://winscp.net/eng/docs/faq_synchronize

I tried updating to no avail so the bug is present in the most recent version as well.

Long story short; everything in "Synchronize options" is turned OFF except for "Update subdirectories" and "Existing files only". More often than not, when a change in ONE file is detected, it uploads the ENTIRE directory as if "Synchronize on start" is enabled. It's a huge waste of bandwidth to synchronize every single time...