Kliment,
I think the issue with the Tracker method is that you are pressing "R". Here is the course of action:
1) Select the object
2) Click your reference point
3) Select the Elevate command from the tracker
4) Drag in either the up or down direction and then type the distance (always a positive value).
The coordinate box still has some functional use and is still popular amongst longtime users but it is not the recommended method of input for the newer versions. The coordinate box does indeed not play well with the changes to the 3D environment but the Tracker does work well here. Let me know if you still have the issue, given my advice.
Best regards!