Good news for those plagued by the recent spate of blinking questions mark startup problems: Conrad Klahn of Apple Technical Support Online writes that Apple is on the verge of posting an update to Drive Setup that should fix this issue once and for all.
He also assured me that the report last time, which suggested that there may be a link between the ? problem and the L2 cache, was in error. He added that there was an L2 cache problem "with some of the early 5500's and 6500's shipping with 6400-style cache instead of the new quick-switch cache. This L2 cache mismatch caused problems loading software. It has nothing to do with the Flashing ?. But this is why they were referred to the Apple dealer to remove the cache prior to the installation of Mac OS 8."
Conrad also implied that the cause of many of these blinking question mark problems is a continuation of an old issue: the hard drive shutting down before the write cache can write the data back to the disk. This is why not shutting down the Mac (or disabling write cache, if your driver permits this) will likely prevent the problem.