Seems strange that this works

tsql -S servername.xxxx.xxxx.net -U username -P password -D dbname

but this doesn't

tsql -S MYMSSQL -U username -P password -D dbname

Try enable logging and using just server name in freetds.conf

  # Whether to write a TDSDUMP file for diagnostic purposes
  # (setting this to /tmp is insecure on a multi-user system)
  [global]
     dump file = /tmp/freetds.log
     debug flags = 0xffff
  [MYMSSQL]
     host = servername.xxxx.xxxx.net
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