Steps to reproduce:
1. Load the save provided http://forums.civfanatics.com/uploads/24121/Jon_Lloyd_BC-1430_BUG_CITY_GOV.CivBeyondSwordSave
2. End turn.

Observation: Worker is automatically assigned to the newly improved cow resource in Bombay 'fat +'.
Expectation: City governor is inactive so workers should remain in assigned tiles.

This was in Epic Game/Marathon with only 'Choose Religion' and 'Permanent Alliances' non standard game options selected.

Definately a bug, happened to me also. So annoying.

I think you're confusing what the governor does & doesn't do. The governor will emphasize commerce or food etc when selected, but will still 'govern' when the emphasize buttons are turned-off. In this case, it changes a 1F/2H plot for 3F/3H/1C - which is a good move no matter what's being emphasized. Why would you not want to work this tile?

K, this save may have not been the best example, point is I've had it happen when a floodplain cottage was just completed and the Governor moved a worker from my only shield generating plot (forested plains hill) to the shieldless better yield plot.

Annoying if you're trying to get stonehenge built ASAP.

And I was under the impression that if the Governor is switched off (irrespective off any emphasis) that city pop. plot assignement should stay where you put them.

Isn't that the point of turning it off?

Well, the governor and the workers actually work together now, and the governor does take note of city size - and will grow a city if it isn't unhappiness-capped, in order to make it more productive. I think that when new plots become available, it will automatically switch, but if you manually switch back, then it won't change them.