Difficult to tell without session log file (please attach complete one).
One possible explanation is that the interval of changes is below resolution of file modification timestamp as provided by the server (FTP servers commonly provide minute resolutions timestamps only).
See https://winscp.net/eng/docs/timestamp

To add to this: I am syncing both machines to the exact same time using NTP, and I've manually checked that the times are correct.

On a Win 8 machine running keepuptodate with a Mac, when syncing 'both' I frequently but inconsistently get the following issue:

I make a change on the windows machine, save it, and the change IS DETECTED but then the file doesn't copy.

Here is the command line:

"winscp.exe" "pants" /console /command "keepuptodate C:\Mirror\mycode /Users/ken/mycode -transfer=binary -filemask=|*.log;*.pyc;*.version;*.pid;/.*;tmp\*"

Here is sample output:

Change in 'C:\Mirror\mycode\config' detected.
Change in 'C:\Mirror\mycode\config' detected.
Local 'C:\Mirror\mycode\config' => Remote '/Users/ken/mycode/confi
g'
C:\...\extensions.rb | 1 KiB | 0.0 KiB/s | binary | 100%
Change in 'C:\Mirror\mycode\config' detected.
Change in 'C:\Mirror\mycode\config' detected. <-- why isn't this copying?
Change in 'C:\Mirror\mycode\config' detected. <-- why isn't this one also copying?

Thanks for any help!