I work a flex tour job for the federal gov't and this happens to me a great deal because my schedule is anything but a "normal" one. I keep a copy of all submitted time sheets. You might ask, why, when they already have that info? You'd be surprised what happens between the time you fill out the time sheet and the time it is processed by payroll. I have had department heads subtract OT hours that I worked, and even remove shore leave days that I earned. On the other end, sloppy transposition errors have cost me. Always the error is in their favor, surprise surprise.

So in future, keep copies of every time sheet you fill out and expect to have to submit again and again. Almost all employers have payroll problems. Many employers outsource the payroll functions making things even more fun to straighten out.

Edit: I see you clock in/out electronically. Still, the above applies. Keep a notebook and record your daily hours and tasks. Recording the tasks you do each day will help justify the hours, especially if we are talking OT or premium pay.