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The only difference i can see between your configuration and the example from the ubuntu site is that you miss the value for the Database key in the server section of your odbci.ini. I mentioned this already. As far as i understood the manual you must provide a value for that key (...yes, i'm skating on thin ice).
Please keep in mind that this is not a perl issue. Read the manual again - with patience. This is something that i can't do for you.
There are a few ways to use Perl to connect to a SQL Server using FreeTDS.The recommended choice is DBD::Sybase from Michael Peppler. Despite the name it works for any Sybase or Microsoft SQL Server...
tobyink already mentioned this, see above.
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In reply to Re^7: [unixODBC][FreeTDS][SQL Server]Unable to connect to data source (SQL-08001)