First question is why bother with such a small file?

RSYNC is not really a byte level sychronisation, it is a "chunk" level sync.

If you are only appending the data to the source file then you can do this much more simply by just comparing the lengths of the files, copying off the right number of bytes from the larger and sending them over.

Have a look a MS SyncToy if it's just the automation that's giving you trouble.

Also have a look at RichCopy (if you can find the binaries) which has some advanced copying features.

Finally, Unison is a cross platform syncronisation tool which looks like it will do what you need.