I don't know why but whenever I plug in my info from my last paycheck to esitmate my taxes (running them through an online service like Turbo Tax) it always ends up a lot higher than when I use the info from my W-2 into the same program later.
One thing to remember is that the online tax prep services may have not been updated with the latest tax info due to last minute bills by Congress to extend certain tax credits. I know a few years ago I had to wait to file as Congress was still debating some tax credits/deductions (college tuition, etc) and Turbo Tax wouldn't even let me file until they had updated with the new changes.
My 2 cents.
Jill in CO