Sometimes you need to calibrate the clicks of your scope with Chairgun - it's not an error in Chairgun, it's an error with the clicks on your scope. There's an option in Chairgun to calibrate your clicks. The reason for this is that just because your scope says it's 1/8 clicks, doesn't mean it actually is.
As has been said earlier the scope height is important - but if you measure the height of the centre of the scope to the centre of the bore, you'll get the wrong answer - that's not the correct method of measuring the line of sight height. Using the wrong method is often the reason why people say that Chairgun doesn't work with sloped mounts. It does work with sloped mounts if you measure the line of sight height correctly.
The actual height you want to know is the height above the muzzle of the line of sight through the scope, not the height of the scope above the centre of the barrel.