Now that everyone has waited three years to hear the solution, here's how I run my tournament. I have a 7:00 start time, with a $10 entry fee. At 7:01, the entry fee is $11, if I can get you in late. At 7:06, the fee is $12, if there's room. At 7:11, the fee is $13.00, if there's room. And so on... If people call, they guarantee their spot, but still have to pay the late fees.
The extra money goes into my break pot. I just make sure to tell people with byes that they may lose them if someone else comes in. Nobody seems to mind, since the late people are punished. And fewer people come in late.
Cory