Thanks Dawn,
after reading your post I went trough the file, checking first permissions and state and after that I went trough the file structure.
I found out that, even though the structure was working correctly from isql command line, it was not correct for Sybase Central. I did not have comma separating the port number and the ssl definition.
Wrong :
[SERVER]
query=tcp,ether,srvname,5555 ssl="cn=commonname"
query=tcp,ether,srvname,5555 ssl="cn=commonname"
Good:
[SERVER]
query=tcp,ether,srvname,5555,ssl="cn=commonname"
query=tcp,ether,srvname,5555,ssl="cn=commonname"
Working perfectly now.
Cheers