I suppose payment in advance is a good policy. Although to be honest, I think most suppliers of race services (timing, PortaJohns, etc.) don't ask for that. It's somewhat the nature of the business that many races don't have much money until they open registration, and that's much closer to race date than they'd want/need the course certified.
Ron, I make the effective date when I submit the certificate, per instructions from above. If it turns out that's after the race date, that's their problem. If some BQs or national records don't count because of it, maybe it will get the RDs off their duffs the next time.
BTW, I think this is generally a rare situation.
To Scott: Could you call the RD and imply/threaten that his race will be "decertified" if he doesn't pay the measurer? Unless he reads this Board, he wouldn't know it's a mostly hollow threat. "It would be a terrible thing if your race was decertified and a lot of runners lost their Boston qualifiers because of it, ya know? They might, ya know, get all mad and write some nasty things on the running message boards. Ya got a nice little race here, we'd hate to see something happen to it, ya know?" You can even give your name as Rocco or Guido (maybe that's why Pete V. uses Guido Brothers as his company name!)