Now you talk about it I seem to recall that Daniel had an issue with MDI, If I recall it was ok if he jogged first but then again I think it was possibly only after a feedhold. Plugin update cured that so it wont be neptunes problem as he is using the latest one but I suppose it could still be related and needing looked at.
Hmm... was that me...? Not sure this is the issue I had, but then may be you just have better memory What I do remember I had is that I was getting wrong moves made when commanded from the MDI. Another problem I had (I think it still exists) was after hitting softlimits while running a program or an MDI command, I was not able to jog that axis. Had to jog other axis to enable this one. The issue with feedhold was a another different problem.
Now I can say this - sometimes I enter a command in the MDI hit Enter and nothing happens. Look back at the screen "may be I missed the Enter key", but can see the command in the MDI history. Going up with the arrow and highlighting the command and hitting the Enter executes the command. Have it happening every now and then, but can't see what's causing it.