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After asking around on the FreeTDS mailing list, a guy called Peter Deacon wrote a patch that adds IPv6. I I did some testing with Perl and after forcefully installing a newer version of DBD::Sybase I was able to successfully connect to my SQL Server 
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With the FreeTDS library now support IPv6 connections, I went to the Nagios Exchange and picked check_mssql_health, which can do rather elaborate checks on all sort of SQL Server properties.
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