How can I judge the extra amount of water to use if I am cooking rice with extras in in my rice cooker?
There shouldn't need to be any variation in the water at all, since the things that you are adding are already hydrated and are not taking in any water.  Indeed, it would be possible that some vegetables might even give off water.

I would be more inclined to look to whether you are measuring accurately every time you use the rice cooker (just asking) and then, if so, whether your rice cooker is consistent.  I had an inexpensive rice cooker that I liked for the convenience, but it was inconsistent on turning off, so the results were a little too varied, OK for me, but not when I was serving other people.

The only other thing to consider is that many rice cookers work on a temperature principle...when the temperature starts to rise (meaning the water has been absorbed) the cooker shuts off.  If the ingredients you are adding are raising the temperature of boiling (as in a lot of salt, say) then it is possible that you cooker is shutting off before the rice is cooked, and then the water is absorbed or evaporates, but the rice cooks no further.

I would pay very close attention to your measuring (rice and water) for the next couple of batches and see if that fixes the problem.