Possible solution 1

I am using jtds driver so I would suggest checkingout their proposed solution first here http://jtds.sourceforge.net/faq.html#instanceGetInfo

Possible solution 2

Their solution did not for me so here is what I did :
From cmd prompt run
sqlcmd -L and make sure that the server you are connecting is listed in the returned list, if its not then there is your problem.
Simply restarting ‘SQL Browser’ and ‘SQL Server’ should work, run you sqlcmd -L command and make sure that your server is visible in the list.