Responding because this answer came up first for search when I was having the same issue:
[08S01][unixODBC][FreeTDS][SQL Server]Unable to connect: Adaptive Server is unavailable or does not exist
MSSQL named instances have to be configured properly without setting the port. (documentation on the freetds config says set instance or port NOT BOTH)
freetds.conf
[Name]
host = Server.com
instance = instance_name
#port = port is found automatically, don't define explicitly
tds version = 8.0
client charset = UTF-8
And in odbc.ini just because you can set Port, DON'T when you are using a named instance.