Thanks for your report.
I have sent you an email with a debug version of WinSCP to address you have used to register on this forum.
I'm currently using WinSCP 5.7, but this problem has occured in earlier versions as well. What happens is that when I have a larger file structure (current project file structure has 279 directories) and try to use "Keep remote directory up to date" it starts out fine, but as soon as I make any change to any local file WinSCP will start running through every file and directory and outputting "Change in [directory/file] detected." I even compare and synchronize the directories before and it shows that there are no differences found. This problem seems to only occur when I'm watching large directories because when I use it on projects with ~10 or so directories it works fine.
I am connected through SFTP and using the options "Delete Files", "Update Subdirectories", and "Synchronize on start" and transfer settings are set to default. Anyone have a solution to this issue?