Hi Boris,
I doubt that there is a pull-up on the computer’s LPT parallel port (although you could possibly have a bad Pin 10). There are, however, often a pull-up’s on the inputs to the breakout board / controller board.
I suggest that you wire your e-stop so that it takes pin 10 to ground with a pull-up to +5 if necessary then configure e-stop as Active Low.
Tweakie.