Changing the svc-syslog netdest doesnt magically make the controller start to use port 5141 for syslog, in fact you need to put that back to udp/514. AFAIK the controller logging directives won't let you change the dest port. If you need to remap it you can add a dst-nat rule in an ACL on the outbound port, or, use iptables input rule on the graylog machine to map 514 into 5141 for the controller source ip (presuming it's linux based)
Additionally, you may find that the syslog is actually going where you expect, just to the wrong port - use wireshark on the graylog machine to check. Also, don't forget that the controller will send various patterns of log messages, all of which are non RFC 3164 conformant which may cause them not to be picked up by graylog by default. There is an option in later s/w versions to change the log format to 3164 compliant, but if you're on a 6xx it may be too old, you can check the docs about it.