As discused time ago, it's common that files don't get updated when synchronizing due to time-stamp problems, even when filesizes differ.
When synchronizing in one way (from local to remote) via command line, ie:
scp ... /command synchronize remote <src> <dst>
SCP is not taking respecting the .ini option "Compare Criteria = File Size". Only "modification time" is considered.
It would be great it this option could be used with "/command synchronize remote", since files are not being updates allways and it is pretty reasonable that .ini directives should work in command line mode too.