Walls reference your story heights not slab heights. If your slabs are not at story height you will have to manually adjust their heights as you have done.
Generally story heights are set at your slab heights, either to core top or bottom depending on local standards. If you have staggered stories, you can create extra story heights to get around half stories and have walls set to alternate stories. The downside of doing this is how your floor plans are displayed but there are ways to get around this which others have covered.
ps. You should include some basic information about your ArchiCAD version and computer specs in your signature as some issues are version/hardware specific.
AC22-23 AUS 7000 Self-taught, bend it till it breaks.
I think famadorian is asking for an automatic way to attach walls to the core of composite slabs when the slab's reference plane is set to TOP (and not core top). Assuming that the story heights are set at slab heights as stated, when using the top of a composite slab as reference plane, the walls will protrude into the finish skins unless an offset is set so the wall finishes at the core top.
With a defined view, preferably set to without finishes or core only, and hiding everything else that would interfere, you can use the "Adjust elements to slabs" command.
In my opinion this is a slight shortcoming in AC, but I get the complexity in implementing something that would work in every case. To avoid this manual offset in walls (as this is not automatic: this will change the offset parameter in walls, but will not update when slabs are elevated until the command is run again. Will work if the story height changes though) I use core top as the reference plane of composite slabs. While this avoids this manual update and in most cases PBC will take care of junctions, there are other problems that surface with the use of core top as ref plane, such as the fact that it is more common to reference finish floor level than slab top level or the fact that ceilings can't be referenced to FFL as well.
I don't know... there could be an option in walls like "extend to core of nearest slab" when the bottom touches a finish skin, or "cut to core of slab" then the top is at the same level o a finish skin. Kind of what happens in walls when there is a door and PBC is ignored when the door is at the same level as a finish skin.