It sounds like one or the other of you is making enough income to jump the tax bracket up from 12% to 22% or 24% to 32%. For example, if you're each making 50k the payroll software thinks withholding 12% ($5000) is enough ($10k for the household)...but you're making $100k household income ($50k EACH) so in reality $20k of withholding is needed...I'm super generalizing here...I realize there are personal exemptions, last dollar bracket and what not. If one of you is making $25k and the other $75k then the $25k spouse really is getting screwed by the payroll software.
I know you said withholding $5000 extra...probably should be more like $500 per pay period.
