My Box 1 is $18K less than Box 5 for my 401K contribution. That is the only reduction that I see. Should Box 1 be $24,650 less than Box 5 if I maxed out both?
Box 5 should already be your gross minus $6,650.
HSA contributions are deducted from SS wages and Medicare wages (box 3 and 5, respectively), but the 401(k) contributions aren't.
To recap: if your gross is 50,000, and ignoring the "smaller" deductions like health and disability and whatnot:
Box 1 = 50,000 - 18,000 - 6,650 = $25,350
Box 3 = 50,000 - 6,650 = $43,350
Box 5 = 50,000 - 6,650 = $43,350