Redleft, I was at an ERP User Conference a few weeks ago and a user asked me almost the same question you have in regards to MDP and Unix.
The one piece of advise I had to the user was in the creation of the .dpf file. Specifically in the Destination File. Try using the option of a “Specific Filename”. Tell MDP exactly what filename and extension you want the output file to be, instead of using the other options. The end user at the Conference was using the “User Defined Format Filename” option here. And as far as I know he wasn’t getting any more outputs to Unix with extensions in uppercase when it should be lowercase, or even combinations of both.
Try this or let me know if you are already doing this in the .dpf creation…