I have the same problem with MACH3 but have been able to see it is correlated with another issue in mach. I'm not sure if it will be the same for you, but here is my experience/solution
Do you notice that sometimes when jogging with shift held down (for fast jog) the shift key acts as if it is stuck down even when you are not holding it down? ie you do a fast jog, then try to do a slow jog, but the machine still jogs fast? if so maybe you have similar issue to me...
if you hit tab to look at the mpg you see a little green square usually go on or off with the shift key pressed/not but sometimes when shift key is not pressed this square is still green and the machine will still fast jog.
When I have mach3 in a state where you I am not pushing shift, but it thinks I am, the MDI will act exactly like you described for me, you can type but not "enter".
so to solve this just tap shift a few times and it will correct itself as to whether or not shift is held down. You can verify by looking at the mpg that pops up when you hit tab that it is cleared, but very reliably 2 taps seems to solve the problem for me at least.
so if you can t hit "enter" to get it to accept the mdi input, just tap shift twice then hit enter again.
i think this may be your issue to since you specified jogging, then after jogging mdi does not work.