A bit tough to explain. In Beta 635, try the following.
Open any tileset. Select a combo where the following arrangement of combos
[center][font=courier][][][][]
[][][][]
[][][][][/font][/center]
... is very recognizable, as well as the combos underneath the second row. Now right-click in the center of the screen to bring up the context menu, and change the Brush Width to 4 and Height to 2. (Hence the little ASCII display above.)
Now click on the screen. Instead of laying out the top row and the middle row, it'll lay out the top row and the bottom row where the middle row should have gone.
Now go to Quest-> Graphics-> Combos, and press Spacebar. Note the change. Now go "Aaaha!" to yourself, because this appears to be what's happening. You figure it out for yourself.
Hit the space bar on the main screen. Does this fix the issue? Or does it reverse the effect, still being wrong, but in another way?
It certainly does fix it, though it's ... Well, I think that the default positioning has reversed itself; Usually what'd happen is that when you open a quest, the first time you view the combo page via Quest->Graphics->Combos, you'd hit spacebar, and it'd lay it out as you see it on the main screen, and you wouldn't have to do it again until you open up another quest or something, if even. Now, I'm not even sure if you have to do that to lay it out as it appears on the main screen. It may start out like it appears on the main screen already.
This may mean that the behavior of the altered brush widths and heights may have reversed too, having gone from the expected layout as seen on the main screen to whatever layout the combo page view may be.
So yes, I'd say that this is a big, moreso in the unfamiliar, seemingly altered behavior that doesn't seem immediately obvious how to fix, considering the unfamiliar effects of the current behavior of the very recent builds.