What do you mean by "one tax?" and "the other"? A Federal return, and a State one? An amended return? Two W-2 forms? You do not get all of your withholding back, just the amount (if any) that is in excess of your tax liability.
First you asked about when you were getting the refund, and now you are questioning the amount. First, has your return been filed AND accepted? And then, what does it say here? <a rel="nofollow" target="_blank" href="https://www.irs.gov/refunds">https://www.irs.gov/refunds</a>
You only file one tax return for all your income. When you have more than 1 W2 you have more income and more combined tax on the total. So the total federal income tax withholding on them is usually not enough to cover both jobs.
When you added more income, your tax liability increased, so you saw your refund decrease. The program begins by giving you your personal exemption of $4050 plus your standard deduction—both of which lowered your taxable income. So you are not being taxed on as much of the income on that first W-2. Then you added taxable income--so the refund went down. Your refund (or tax due) is based on the total of your income, not “per W-2.” Wait until you have entered ALL of your income and deduction information. You can't really tell anything until it is all entered. That “refund monitor” does not mean anything until everything has been entered.
The IRS gets copies of those W-2 forms, so will know if you fail to claim one. I'm not sure why you would expect to get everything back, as the government would go out of business if everyone did that.
