Sorry, I had forgotten about this posting since payroll at my company actually never got back to me, and I actually ended up figuring out regardless.
Tom had it right on his first assumption and my W-2 was actually correct. My confusion arose from comparing my total proceeds from sales to cover reported in my brokerage/1099B and what was reported in box 2 of my W-2, which is ONLY federal tax withholding. I was hung up on why my total proceeds were barely more than my federal withholding in box2, and the difference did not equal my paycheck withholding total. I realized after digging through more statements that the proceeds were actually correctly distributed across all taxes (state, SSI, etc.), so the total amount was accounted for.
