This is the same behaviour described in #1665, but seems to be caused by the fix for webkit on DomEvent.js.

Reproduced here:
http://jsfiddle.net/n6sZW/
The body is RTL, and so on webkit the mouse position reported is false. Evidence can be seen by clicking on the map and the popup appears at the perceived (false) mouse position.

Overriding documentIsLtr to always return true fixes this:
http://jsfiddle.net/XSaFU/1/
In this example, clicking on the map shows the popup at the correct place, implying mouse position is correct.

Is the webkit fix on DomEvent.js still relevant?