Why won't 432 mege polys?

I've tried everything and I'm going back to 428 if I can't figure it out. I used to just be able to right click and merge polys and now it doesn't seem to do anything. I tried starting a fresh map and making a simple 2d shape with the 2d editor, something that created those crosssections. I extruded, right clicked on the red builder brush and did a polygons merge. Then subtract and, yep, you guessed it, polys on the ends are still seperated. I even tried doing a transform permanetly then doing a merge polys but nope, that didn't work either.

Well apparently I figured it out although I'm not happy, apparently this was done on purpose but now you have to align all the polys that you want merged to the same direction. They don't have to be lined up or anything they just need to be running the same direction. I guess this is a new "feature" that allows you to be more selective about what polys you want merged incase you have many on the same plane like in terrain or complex shapes. In the past I've only needed to do this once so I kept the polys seperated but I've merged hundreds of brushes so I can't see how this will help since you now have to align twice and stick a rebuild in between. You can't even merge the red builder brush before you add it to your world. Just for once I wish that when there was an update to how something worked Warren would leave the old way in as well. How hard is it to to have just changed the menu to "merge all co-planer" and then just add a new menu item for "merge selectively" or something like that. Instead we loose the old way completely and are force to use something we don't want

Align to floor will align on your floor textures so they repeat properly. Back in the doom days the floor had a seperate hidden gird that the floor texture got aligned to no matter where they were in the level. even if the texture weren't touching each other they would still be aligned to the grid, that way if they did have a complete set of floor texture between them you would see they still are lined up to each other in a pattern. Align to wall doen't do this which I wish it did or at least had another button. Align to wall just turns all horizontal textures that are selected perfectly right side up as you see them in the texture browser, the align pan will line up wall textures so they are at the same level in case adjacent ones are panned higher or lower than the others. Unalign just puts the texture back to a aligned to brush state. Although this doesn't seem to work after you align to floor