@rstanley - I think you have hit the nail on the head there.
Without knowing the exact details - it does sound very much like a "conio.h" related problem. An all to common stumbling block that people come across when trying to port older Windows/DOS applications to Unix-like OSes.
I am aware of a few small projects on various code-sharing sites which attempt to provide a Linux implementation of typical conio.h functions. From what I recall, most of them just use ncurses to implement similar functionality - so for example clrscr will use curses and terminfo/termcap to determine the ANSII escape sequence required to clear the screen and will then use curses to output the escape sequence to the screen - thus clearing the screen.
I haven't really taken a good look at any of them, so I don't know how complete or portable any of them are, but one of them might help the OP to port their application with minimal changes to their code-base.
@OP - try searching for "conio for Linux" - I'm sure you'll find one or more of these projects. Even if they are not complete, they might contain some more portable implementations of common conio functions. Couldn't hurt to take a look!
You are going to have to do some porting to get equivalent functionality anyway. If somebody else has already done a lot of the grunt-work, you can just piggy-back off their efforts! (At least, assuming that your code and their code are distributed under compatible licensing terms!)