Well the best way would be getting rdate to work with Windows. If you don't have Cygwin on your Windows server, then you can follow the instructions that will allow you to get sshd up and running under Windows at http://pigtail.net/LRP/printsrv/cygwin-sshd.html
I'm actually not sure if rdate is installed by default. I don't have a Windows computer handy to check.
The instructions are written for XP but I used them equally well with 2000. If you have 2003 then follow the link in the 2nd paragraph on the above site. These will not work with 98 since, as far as I know, it doesn't recognize 'services' and instead uses 'background' processes (?)
When editing the environment variables you can add them as user variables (as opposed to system variables) only if
- you boot up the computer to your user account, or
- you want only your user account to be able to use sshd.
Note that all users will still have access to Cygwin though...
After you get sshd running you can log on from the linux computer, using for example ssh. Now you can synchronize the two computers the same way two linux boxes could be synchronized.