I suspect that entering parts of each job as separate jobs might be throwing the calculator off.
No calculator is going to be 100% accurate, but you might get better results with the IRS Tax Withholding Estimator that NCperson suggested. If you use the IRS Tax Withholding Estimator, follow the instructions it gives for what to enter, and don't pretend that one job is two jobs.
You do have to redo the estimate when something changes. Each time you or your wife gets a raise or a new job, redo the Tax Withholding Estimator after you get your first paycheck with the raise or new job.
