Hi pythonguy,
Hmm. It sounds like AutomationDesk is sending EOF signals to your scripts without being asked. I can't think of a really good way to explore this problem without my own copy of AutomationDesk (I don't have one). It's commercial software, right? You're probably better off emailing the dSPACE tech support people; I'm sure users have run into this sort of thing before.
I can think of a few kludgy solutions in the meantime, though. One thing you could do is replace raw_input with a function that pops open a Tkinter input-collecting widget. The idea here is that the widget would collect input from the user, write to file, close, and then the function that called it would read what was written and pass it back as input. Horribly inelegant, but if you need a quick fix I guess it'll do.
Sorry I can't be more helpful.