Deductions from payroll for personal charges on company credit card

I've run into a problem with how to make deductions from payroll for employee purchases made on company credit cards. (We're processing payroll using QuickBooks Pro 2006)

So here's the specific scenario causing the trouble...

We occasionally have employees who make personal purchases on their company credit card (usually for gas because they're so short on cash that they can't make it to work otherwise). When it comes time to reimburse the company for their purchases, we take a deduction from their mileage for that pay period.

This system has worked well, but occasionally we have a situation where the employee doesn't log enough mileage to cover their fuel purchases. How does everyone else handle repayment of personal charges made on company credit cards?

Is it better to just keep it separate from payroll and require that the employee cut a check back to the company at the time payroll is issued?

Any insight would be greatly appreciated.