OK , the taxes did result in a "net check" to you, everything's good.
"but I still can't fathom how the IRS knows that in addition to the $5864.60 (Cash portion reported on the 1099B) I also received new stock in the new company..."
On a "normal" same day sale of employer stock the broker is not obligated to send you a 1099-B. So in that situation the IRS doesn't really know if you ended up with "cash" or "stock" or some mixture in between. And you don't routinely report your purchases of stock that you make through your broker, right? The issue of the stock you received will come up, down the road, if you sell it. You've got "this years" income properly stated and that's all you're obliged to do.
