The segmentation is normal it's a default in ARCHICAD, unless you use magic wand. If the wall and and slab start on the same corner and finish on the same corner then the segments should line up as illustrated in my screen shot 1. ( blue lines when you select an element and zoom in )
The only reason I can think of with your section not lining up is that the slab and wall don't start on the same corner. Illustrated in 2nd screen shot. ( red lines slab segments locations, yellow wall segments locations )
If you unlucky and the segment of the slab start half way compared to the wall, then you sure see it in the section. Saying this for buildings it is probably way within the aloud margin.
Cheers Carsten
Carsten
www.asmtechbase.com
https://www.youtube.com/asmtechbase
AC 3 to 26 -Windows 7 - 24GB - 8core 4.4Ghz