Hi Lordfox, so probably one reason why you were getting different results was that you were picking on slightly different areas of surfaces each time.

The pick points where you click each surface is significant for Flow, so you will want to pay attention where you are clicking on each one. See here for an explanation of where to pick:
http://moi3d.com/forum/messages.php?webtag=MOI&msg=5853.1

This is a pretty common area of confusion for using Flow, I'm thinking of trying to rework this a bit before V3 is finalized.

Then for doing booleans like Burr mentions the booleans will have some difficulty if your new pieces have bottom faces that are just sort of barely skimming along the surface of the main object. Try sinking the objects down a little bit into the base plane so that when they are applied onto the curved object, they punch a little ways down through the outer surface instead of having a skimming common surface area.

It can be ok to have common surface area in booleans when the common areas are very very accurate to one another like with only 2 planes being the common area. When it's the result of some fitted operation it's easy for the common surface areas to just very slightly wiggle in and out of one another making a highly complex intersection curve which will gum up the booleans.

- Michael