I'm in a similar situation, where I became eligible for my company's 401k October 1st and am contributing as much as possible between now and the end of the year. I set my contribution level at 99% (the max), and got my first paycheck with that arrangement today:
Check Date 10/09/2015 Net Pay 0
(I can't believe I'm so excited about
not getting paid.) : D
It looks like the payroll processor deducted medicare, social security, and health insurance, then sent the entire remainder to the 401k (which is perfect). There was no federal or state tax withholding because the entire paycheck got allocated to pre-tax things, so there were no earnings to tax!
TL;DR: my job's payroll company handled it correctly. I see no reason why figuring the math should be your problem as an employee, rather than than theirs as accountants.