1. Increase the profile timeout
2. The user specified in the database connection was incorrectly specified.
It was DOMAIN.xx.yy\username when it should have been DOMAIN\username. The user was verified using the xp_logininfo sql command
This is the query used for long_queries: (what are the results when run manually?)
"SELECT r.session_id spid, s.host_process_id hostid, s.host_name, s.login_name loginname, s.program_name, (convert(dec(15,3),r.cpu_time))/1000 cpu_time, (convert(dec(15,3),r.total_elapsed_time))/1000 elapsed_time, convert(varchar(3000),isNull(SUBSTRING (st.text,1,3000),'n/a')) as sql_text FROM sys.dm_exec_sessions s, sys.dm_exec_requests r CROSS APPLY sys.dm_exec_sql_text(r.sql_handle) as st where s.session_id = r.session_id and r.status = 'running' and s.session_id <> @@SPID"
3. Please check if the user has permission to run this query.
In older versions, the probe ignored the configured user and used the administrator user by default to establish the connection with the database.
Hence you did not see this problem.
sqlserver probe - Access Prerequisites
Double-check the following permissions with the db admin to be sure that they are in place.