During your sa/isql test, how did you exit from your sessions? Did you type 'exit + go', hit ^S, hit ^C, something else?
Are you running your sa/isql test from the same linux host where the ASE is runing, or from another host on the network?
Is your isql session connecting directly to the dataserver or are you going through an intermediary service?
Are there any login triggers on your sa account? (See the output from sp_displaylogin sa)
Could you run your sa/isql test again, but this time:
session #1: log in as sa using isql; stay logged in
session #2: perform your login/logout test using sa + isql
session #1: periodically run 'sp_who' to see the active connections; does the list of connections grow over time?