@David SR The problem you discuss is different from others in this thread. The short answer to your problem is that withholding and estimated taxes are two different things. DO NOT REPORT ANY MONEY WITHHELD AS ESTIMATED TAXES. (So you will need to go back and delete that amount you are saying you reported this way.)
Withholding is reported to you on W2's and 1099s you receive from people who paid you, but kept back money to cover income taxes you might owe. They give this money to the government and then the government credits you for that money on your return.
Estimated taxes, as well as any refund due you ask the IRS to apply to next year's taxes instead of giving it to you now, are money you send in yourself to the IRS, generally quarter by quarter, although you can send it in at any point and it will be credited according to when it is received.
The IRS thinks of these as two different things, even though they both are ways of paying the taxes you expect to be due when you file your annual 1040.
