Was going to say perhaps it was because of zoom, but that would be out as far as the next star... in pixels.
Might try resetting preferences.
I opened all the .xml files and checked against other projects and didn't see anything out of the ordinary. I reinstalled C2 and it didn't help.
Another thing that is happening is that new objects on the "HUD" layer have this weird offset:
But again, this only happens to new objects, and only in the "HUD" layer. But the "HUD" layer has the exact same properties than other layers (parallax is "100,100", parallax in editor is "no", etc)
PS: as I was writing this, I found out this last bug was happening because one object had the "Color" effect... so nevermind that I guess
The first bug still happens, and I found out it only starts happening once I try cloning something or creating something on the "HUD" layer, and then it starts happening in all layers.
This is the xml for the layer, minus the instances:
(<instances> do close, its just that Notepad++ hid that)