I have an employee with $6000 gross wages and 4 allowances on W-4. Here's the way I calculate fed w/h...
Annualized GW: $312,000 ($6000 x 52)
W/h Allowance: $17,200 ($4300 x 4)
Wages subj to W/h: $294,800

In Pub 15-T W/h Table, $294,800 between $184,950 and $342,050, so w/h $29,502 + (24% of $294,800 - $184,950 = $26,364) = $55,866 ...
$55,866 / 52 = $1,074.35
PayWindow calcs $1,014.79

I'm pretty sure PayWindow is right, so where am I missing it?