What I've seen/heard of (don't race mx) is not scoring anyone who doesn't provide a flagger or do a shift, having entries put into a hat & pulled out if required - they get their money refunded but don't get to race. The 2nd option would either motivate folk to provide a flagger or turn people away. It has happened where one of the top racers couldn't race on the day because his name was pulled out, but that was just tough. I'd guess in that case (or other racers) they'd get an average result if it's a series rather than no points, but again, I don't know.
I do recall the first enduro I ever went to, they refused to start the race until they had enough people to work the checks, which I thought was fair enough, even though it meant that I didn't get to just sit around and do nothing. Then again, it's meant I've worked a check or done something at just about every enduro I've been to.
If you've got to start getting tough, get tough. Instead of this being your problem, this should be the racers' problem and you have to put the ball into their court so they can sort their **** out.
Oh, another thing I've heard of is refusing entry to people who either don't front up for their turn of supplying a flagger or being a flagger.
Again, I'm not sure how it works, but it's an option (no, none of them are nice but until people realise that it's a real dilemma for the club, they're going to sit on their butts & ignore you, when you start hitting back at them, they'll start thinking or heading for the hills).
Good luck & hope it works out (something).