I have noticed over the last few days that the number of flags remaining has been increasing. When I flag a question, it appears that I start at 13 now.
So, what would cause my number of flags to go up?
I guess I should have searched all of the meta sites...
It turns out that there is a formula used to increase the flag quantity based on activity.
You start with 10 flags per day.
Based on your reputation and flagging history, you can end up with as many as 100 per day.
Currently, that means you get an extra flag per day for every 2000 reputation points or 10 net helpful flags (helpful-unhelpful).