The zhēng reading comes from the traditional glyph
癥, a traditional-medicine term for a hard lump or blockage in the abdomen. The metaphor jumped from medicine into general use:
症结 literally 'lump-knot,' now mostly 'the crux / blockage of an issue.' The 1956 simplification merged
癥 into
症, so the tone is the only thing distinguishing the two readings today.