Well, nevcairiel just said that Ctrl+R still works, so it seems specific to Ctrl+J. I can only imagine that someone else is already hooking and consuming Ctrl+J, so madVR doesn't see it. FWIW, on my PC Ctrl+J works just fine in MC17.
Since it seems to be specific to Ctrl+J: You do have a Ctrl+J shortcut in MC? Can you try removing it to check if that fixes the problem with madVR? In any case it would be very easy for me to add an alternative key combination in addition to Ctrl+J, e.g. Ctrl+Shift+Alt+F12 or so, until I get around adding key customizations.
I've never used WM_INPUT before, but I have a hard time believing that it totally breaks WH_KEYBOARD_LL. If all else fails we can do a custom interface or whatever else is necessary, but since (according to nevcairiel) the problem is specific to Ctrl+J that shouldn't be necessary.