Hi Martin, yes boolean union does some additional work to find coplanar faces being unioned together and merge them into larger single planes. It looks like something is not quite going right with that process as I would have expected all of those pieces to be merged. If they are at a very slight angle to one another that may be the cause.

It shouldn't really cause any problem to have only some of them merged but if you want a symmetrical result it sounds like you've got it figured out now (thanks Stefan!) that you can use Join instead once you've removed the centerline faces so you have unattached edges down the middle. Join will not do any planar face merging.

If you can e-mail (moi@moi3d.com) the model that did not merge all the faces with boolean union I could try to take a look and see if that could be fixed up. It's a little hard to give a way to turn off the merging because boolean union doesn't necessarily have any steps in it where it waits and shows options.

- Michael