In older Netprobe versions, there was a known issue with SQL-Toolkit plugin when trying to connect Microsoft SQL Server. The port setting was ignored, and the plugin was able to connect default port 1433 only. Users should upgrade to Netprobe version GA5.6 and above which include the fix COL-1674.
Workaround for older Netprobe versions
Users may try to append a comma and put the port number to the Server Name field:
Where you have
Server Name: HOSTNAME
Server Name: HOSTNAME,PORT