That may be due to the way you edited the start_zones table. Rather than editing that, the usual way to set a starting zone for all new characters is to set startzone in the variables table:
Code:
INSERT INTO `variables` (`varname`, `value`, `information`, `ts`) VALUES ('startzone', 'befallen', '', NOW());
South Qeynos is ZoneID 1, so the code probably defaults to that if something has gone wrong. Maybe there is something in one of your log files to indicate the problem.