Okay, by checking and unchecking and checking and then fiddling around with order of the folders checked, I've gotten files to show up. So whatever might have been the original problem there (the check boxes are so tiny on my screen at 1024 res that it takes a careful look to determine their checked state), fiddling seems to have undone it and it's working as I would like. That options area was, I'd guess, definitely the source of my problem.
As for the other problem, the opening of the options window when I open the search window, that has not been as satisfactorily resolved. Yes, when I open just the options window, by right-clicking the systray icon and selecting options, I can dismiss it by clicking that close window button. But that doesn't prevent it from re-apearing next time I open the search. In fact, it opens first and then the search opens on top of it (when I use the custom key, the pause key, or the right-click menu for the icon), and it disappears when the search window is dismissed. If I bring the options window to focus by clicking on it, it properly comes up on top of the search. Then if I click that right corner button to close the options window, it blinks out and immediately reappears again on top of the search. In other words, I cannot dismiss it while the search is open although I can close it if I open it alone.
FWIW, I'm using a fairly vanilla Win2k and shutting down, one by one, all of my running programs except for NOD32 and ZoneAlarm failed to affect this behavior. But shutting down FARR and restarting it a couple times (once, yesterday, didn't do it) now has, for the moment, managed to let me get a search window by itself again. If it resumes, I'll try to record the circumstances and let you know so you can see if it's reproduceable or just some random moment of cosmic injustice.
Thanks for the help.