The x coordinates of the Position File need to be inverted for the bottom layer. Let's say that you picked the left corner for your position file as the origin. In PCB new the coordinates are of the same sign for the top and the bottom layer because you are in the "see through" view. However when the board is flipped on the pick and place machine your top left corner now became top right corner and all X coordinates now should be negative.
And another suggestion. For the ascii position file the separate fields are delineated with spaces, so during file generation all the spaces in all the fields used need to be replaced with underscore. Not sure about other fields, but I personally use spaces a lot in the value field (i.e. designate voltage of a capacitor or precision, like 47uF 50V) If those spaces are not replaced the file will be corrupted when imported into a pick and place machine.
The most annoying thing about ASCII position file is the fact I never saw any official documentation about this format.
Any official info is welcome.