Thanks. What protocol are you using?

No, it wasn't that. I found out by switching to Filezilla. I had foolishly and erroneously uploaded the files once with an all lower-case name, for example chapter01.html, (which was what I wanted) and once with an initial capital letter, for example Chapter01.html, which was an error on my part.

In the Unix world these are legitimately two different files, but WinSCP somehow swallows the duplicates, and only shows the lowercase name, but with the the uppercase file's details, whereas Filezilla correctly shows both. I deleted the ones with capital letters from within filezilla, and now everything is just as I'd expect. I suspect this might be classed as a bug, albeit a very unimportant one.

Size difference: You are probably using text/ascii transfer mode..

Though it should not matter for synchronization.
Try reading this FAQ:
https://winscp.net/eng/docs/faq_synchronize

I am maintaining a collection at ibiblio.org, and am using winscp to update it. I thought it would be simple to use "keep remote directory up to date" and make sure the local directory only contains files I want to update. So I use BeyondCompare on the local side to keep a mirror site up to date, then I open winscp and switch on "keep remote directory up to date" from that mirror site to the ibiblio ftp site.

My idea was to minimize the amount of data I send to ibiblio each time I update. The trouble is, I have noticed that two particular folders always copy along with ALL their contents, even though they have not been updated for quite a while, and then I noticed that the local and remote file sizes for all my files are different by a random number of bytes for each file, sometimes as much as 200 bytes different, other timers only a few bytes.

Have I misunderstood something here? Why are the file sizes different, and what is the defined behavior of "keep remote directory up to date"???