Employee Not showing up in "Create Payroll"

I think I messed up...

We have an employee who gets paid on commission.  The commission amount usually gets paid with the normal payroll run.  I did a special check for him and paid an individual through payroll.  All worked fine, except...

Now, when I go to process his salary, his name doesn't show up.  It must be because I just processed a payment to him, but his salary was not paid.

Anyone know how I can work around this?  Create another individual paycheck separate from the batch payroll for other employees? 

We just ended our Gold Support, so now I am a fish out of water.  Any help would be much appreciated.