Blair;
The startup state level of the digital lines of any E-series board is high impedance state. So, either there is something wrong with the board itself or the external circuitry you are hooking up to the board is doing something that is changing that behavior of the board.
I advise you, first, to hook up a scope to the digital lines to double check if the board, without being connected to any external hardware, is behaving like that or not. By doing that, you will be able to narrow the problem down to its cause.
Hope this helps.
Filipe