Microsoft SQL Server Connection problems

I have a weird situation in that my transform has 3 steps that require a connection to a MSSQL Server. The transform is failing with the following errors

Error connecting to database: (using class net.sourceforge.jtds.jdbc.Driver)
Network error IOException: Connection timed out

I am using the latest sqljdbc4.jar file. The Connection tests OK in PDI.

I can run the job perfectly with only one step in the transform (one connection) but when I try and run it with the three steps it fails in the initialisation stage.

I can run the job perfectly on my desktop (Ubuntu 13.10).

The job is failing on our PDI server (Ubuntu Server 10.04 LTS). The job used to work but now does not.

Any suggestions because I am all out of ideas.