Bugs are missing from queries, but exist in the database (and I can pull them up by specifying the bug ID). What is wrong?

You've almost certainly enabled the "shadow database", but for some reason it hasn't been updated for all your bugs. This is the database against which queries are run, so that really complex or slow queries won't lock up portions of the database for other users. You can turn off the shadow database in editparams.cgi. If you wish to continue using the shadow database, then as your "bugs" user run "./syncshadowdb -syncall" from the command line in the bugzilla installation directory to recreate your shadow database. After it finishes, be sure to check the params and make sure that "queryagainstshadowdb" is still turned on. The syncshadowdb program turns it off if it was on, and is supposed to turn it back on when completed; that way, if it crashes in the middle of recreating the database, it will stay off forever until someone turns it back on by hand. Apparently, it doesn't always do that yet.