Hi Martin,
As far as I remember 'Clock Sync' assumes you have the correct 'SET TZ= ' in the config.sys, it does not put it there (see set tz in the command reference) and it does need the second version you show. Just think yourself lucky you don't have something like I need -
SET TZ=CET-1CDT,3,-1,0,7200,10,-1,0,10800,3600