I remember when UBB first came out with the PHP accelerator, the instructions said that the entry page should continue to link to ultimatebb.cgi, not ultimatebb.php. Is that still the case?
Yes, it is. The user should be redirected on first visit to ultimatebb.cgi even if linked to the .php page, but if that doesn't happen all the bulbs in forum summary and forum page will be yellow.
Most chances are that the UBB will redirect them automatically to the .cgi page; even if not, it won't cause any long-term damage, only that in this session they'll see yellow bulbs also for old messages...