Doubt there's a bug here. First, "x" is not a true Allegro command, it is an alias that is defined by default to be aliased to the "pick" command. So check that this alias is still the same, since it is easy to change it.
Second, I'm not sure what you mean by mounting holes, are you using a footprint or simply moving a via that you call a mounting hole?
Third, Allegro lets you move things by several different references, but the info will give the x-y origin.
For example, you can define a mounting hole symbol that contains a through hole pad. Simple. The symbol has a 0,0 origin, but you can place the pad anywhere you want inside the symbol, for whatever reason.
So... you can move this footprint by the symbol origin in the layout, but if you do "info" on the pin instead of the symbol, you'll get an offset.
Then of course, Allegro has etch and non-etch grids. Also, be careful in the setup. I've seen people converting mm to mils and playing with the accuracy and converting units a few times (playing around, I guess), and suddenly the whole database goes on a weird set of dimensions that can only be reset by refreshing all the symbols.
Check all that before submitting a Cadence bug report.
