The reason is that WinSCP considers remote path with syntax like /xxx/xxx as an unknown switch, not as parameter.
Until 4.0.x WinSCP considered only /xxx parameters (onw shash followed by letters) as switches, so it was possible at least to use paths with two slashes like /xxx/xxx. WinSCP 4.1.x considers any parameter starting with slash as a switch.
We should revert to 4.0.x behaviour.
However 4.1.x allows you to use switch // to denote that all following parameters are not switches. Hence command like below can be used as workaround:
winscp41x.exe /synchronize c:\localpath // /remotepath