"I have a somewhat similar issue."
Really, you have the EXACT SAME ISSUE, with a twist. You've calculated compensation for 3 lots of ESPP shares but your W-2 is reporting compensation for only 2 lots. The "twist" is that according to your W-2 you DON'T HAVE a QUALIFIED ESPP and the shares AREN'T "ESPP" shares. Why do I say that? Because the description for that code "V" next to amount in Box 12 is "Income from exercise of NONSTATUTORY stock option(s)". Income created by the sale of stock acquired via a qualified ESPP just shouldn't be reported in Box 12 with a code of "V".
It's tax day tomorrow so I think you'll have to let that "code V" issue slide for the moment, and I'd guess it's a mistake on the part of the payroll department that prepared the W-2.
If I had to make a guess I'd guess that the one lot not mentioned is considered a qualified sale, at least by the payroll department, and I'd simply handle it "as such" and use one of the work around methods mentioned in the answer.
