I've had the popup issue, and it can be very annoying. Enter a minus sign, a zero and then a period and you get a popup each time saying "Please enter a number" or something similar. So you have to hit enter, and rather than just continue typing, you have to click back in the box because MPE has highlighted that whole entry again. Makes entering negative numbers less than 1 a problem. I tended to just start entering the number as a positive and then going back and adding the negative. It's a nitpicky thing, but highly annoying if you're doing a whole bit at once that's on the bottom or starboard side of a ship.
Your best bet is to use MPE and deal with its eccentricities.