For security reasons we do not run our SQL Server on standard SQL ports. There is not a way to specify what port to use for MS SQL. Also this would be valuable for MySQL as well.
Upon further investigation, it appears that if you change your server name to something like
IPorServerName,PORT
it may work just fine. Note that it's a COMMA that separates the port from the server
Yea shortly after I posted that, I thought that might be the case.