You are wrong in your analysis and there's no way that "fixing" last year's W-4 will change a thing.
Even in a situation where you worked two jobs, got two identical W-2's - same wages, same withholding - the way the income tax return works from a "mechanical" perspective means that the 2nd W-2 entered will result in less of a refund change than the 1st W-2. And in your case the 2nd W-2 seems to have reported the same income as the first one but less withholding. So, everything else being equal you'd expect that you wouldn't get the same "increase" in your refund as you saw when you entered your 1st W-2.
There's absolutely nothing you can do about that now. What's done is done because all the W-4 does is affect your withholding for the year, and the year is over.
Tom Young
