A handy little utility from Canadian Nicholas Geraedts is SyncToyHidden.exe
It will let you run a SyncToy job without popping up the GUI.
His site is down sporadically, so here is the content
The more work I do, the more paranoid I become of possibly losing it all. I’ve got a pretty elaborate hardware setup in terms of disk storage, but I was lacking a simple, functional tool to do the backups of the data on a regular basis. I looked at Microsoft SyncToy for the backups, and it seems to do everything I need/want it to, except for one – scheduling. Their help documentation tells you to use their command-line application and the built in scheduler. This seems to do the trick, but there was one snag – it shows the ugly command prompt. This simply wouldn’t do….
I fired up Visual Studio 2008 and started writing a simple little .NET app to act as a wrapper for the command-line window. At the moment, it just runs all of your folder pairs, but I’ll be expanding the command line parsing to search for specific pairs. You’ll need the .NET Framework 2.0 installed for the software to work. Simply extract the file into the SyncToy directory, follow the help instructions for setting the scheduled task, but replace the program path with the following:
“C:Program FilesSyncToySyncToyHidden.exe” /hide /quiet
Obviously you’ll have to replace the path with the one that’s relevant to your system.
Please let me know if anyone runs into any troubles with the software.
P.S. Thanks to jcarle for the help with the command line switches.