Dear Naftali,
I suppose you are using ArchiCAD 8 (or newer) because this is a behavior introduced from this version.
The way in which ArchiCAD clean up the intersection is based on layers intersection group numbers (you can define them in the Layer Settings dialog window.
A simple workaround is to use the add-on named "Intersections in Combos" located in the goodies folder that let you change/handle this behavior in a simpler way.
friednly
Fabrizio
Fabrizio Diodati
Graphisoft Italy Srl | Via Rossignago 2/A Spinea Venezia 30038 Italy