I've noticed a problem where if I have more than one tab in a window. When make a different tab the active tab, the line numbers displayed are those from the tab I just left. I can always reproduce this.
In the case I'm experiencing at the moment, the file in the tab I'm leaving is only 24 lines long and so has no need for scrollbars, where as the tab I'm activating has many lines. I scroll so that line one is not visible. I then change to the other tab, then change back again. I see line numbers starting at one. But it is not really line one that is being displayed. If I Cmd-UpArrow. The line number display is again in sync.