This is a known problem with rclone at the moment, one which should be addressed in the next couple of releases.
In the mean time there is quite a good work-around.
You can do a "top-up" sync like this
rclone copy --max-age 1h --no-traverse path/to/source remote:path/to/destination
The --max-age 1h will mean that only files younger than 1 hour will be copied and the --no-traverse will mean rclone does not look through the entire destination file tree.
Note that this uses rclone copy not rclone sync so it only copies new file, it doesn't delete any files on the destination.
This works very well for backing up recently changed files quickly. You still need to do a sync to propagate deletions but you can do it less often.