I upgraded from 1.0 to 1.2.3 recently and since then the cursor is always two columns ahead of the current character. The indicator at the bottom would show 1:1 (row 1, col 1) but the cursor would be on the third column.
Screenshots – notice the position of the cursor
This is the sequence of keys I pressed:
Screenshot 1: 123
screenshot 2: [left arrow] [left arrow] A
In screenshot 3, [right arrow] B
These are the only keys I pressed.
OS: ubuntu 15.04
Upgraded through the .deb on atom.io not through package manager.