The command isn't passed directly to windows, it has to be run through the command parser first, which means that quotes will get eaten, so you'll either need to wrap the --message portion in a set of quotes that can be eaten without any issues, or you'll need to escape the quotes. This version should work:
command="exec '^(...*?):([0-9]*):?([0-9]*)' svn ci '--message="automatic checkin"' '"$File"'"/>
You can see how the command is interpreted by looking in the console afterwards.