IMac sometimes beeps endlessly after wakeup

Question

I'm not very familiar with Mac computers, though I'm very experienced with Windows computers, so I might overlook or misunderstand things obvious to someone more familiar with Macs. I'm helping a less technically-oriented friend with her Mac. I'm not sure I have all the information that is needed, but let's try.
The computer is a fairly old one-piece iMac. The "About" choice under the Apple menu says it is an iMac 5,1 and SMC version (system) 1.8f2. The current OS is 10.6.8. I believe the original OS was one of the 10.4 versions. The computer originally used a wireless keyboard and wireless mouse, both from Apple. Sometime after the upgrade from 10.4.x to 10.6.8, the wireless keyboard and mouse were replaced by a wired keyboard and mouse. There is an HP inkjet printer connected to the computer. The owner of the computer is not certain of the timing, but believes the beeping that is the subject of this post started after the switch to the wired keyboard and mouse, but she admits that it might have started before the switch. She is confident that it started sometime after upgrading to OS 10.6.8. She was told by the staff at an Apple Store that she needed to upgrade to OS 10.6 in order to use Skype, or some new version of Skype (I am not sure about that reason).
The problem is that, at times, the computer will emit one beep or a series of beeps (the owner sometimes calls them clicks, but I have heard them and would use the word "beep"). The owner has reported only one situation in which a single beep occurs.  Usually, it is a repeating series of beeps, each of the same duration (about half a second or maybe a little less, I'd say) and with a uniform interval between them, though I can't say whether the interval between the beeps is the same as the duration of each beep.
The beeping usually starts immediately after the computer wakes up from the sleep state (done by pressing a key on the keyboard). The owner usually puts the computer into the sleep state when she is done working for a while by selecting Sleep from the menu. I imagine it sometimes goes to sleep on its own due to exceeding the configured time of inactivity, but I have not asked her that. Sometimes the beeping does not start immediately after wakeup, but when a folder on the desktop is opened. When the computer is emitting a series of beeps, the beeps usually can be stopped by opening Safari and starting to type a URL. Typing the first letter of the URL stops the beeping. The owner is not sure whether starting any other program also can stop the beeping. If the beeping started when a folder was opened, usually closing the folder makes the beeping stop. The owner says that she thinks opening a folder containing Word files causes the beeping (though that does not trigger beeping all of the time), but most of her folders contain Word files, so I'm not sure it actually is necessary for there to be Word files in the folder to trigger the problem.
When the computer is emitting the series of beeps, the owner reports that the menus respond differently than normally. She says that, normally, when she clicks on a menu, it stays open while she makes her selection from it, but when the computer is beeping, she must hold the mouse button down while selecting her choice, else the menu will close.
The beeping does not start after every wakeup, but once it has started beeping after a wakeup, the beeping starts at all subsequent wakeups until the computer is shutdown. The owner does not know whether a restart rather than a shutdown also stops the beeping after wakeup. When beeping occurs after a wakeup and has been stopped by starting Safari, the owner believes that the computer does not resume beeping again until it has been put to sleep and is awakened again.
The owner has not had the computer start beeping right after being turned on, however, it sometimes does emit a single beep when the first letter of the user's password is entered into the logon dialog box. This single beep did not occur on a test of using the logon dialog after logging off without shutting down. (The owner does not usually log off, but I had her try it just as an experiment to see whether the single beep would occur when logging on in that situation.)
Possibly related is that there have been times when Word documents will not open. The owner mentioned that when this happens, if she hovers the pointer over the Word icon in the dock, she gets a choice to force quit. I believe she said that using the force quit restores normal operation of Word. There also has been at least one case in which Safari refused to close. I don't know how common this sort of stuck program is in a normally-operating Mac, and I don't know how often it occurs on this Mac.
When I was observing once, when I asked the owner to log off, the logon dialog box proceeded to shake rapidling left and right a small distance (perhaps a centimeter or so) while the computer emitted a series of beeps different from the other series of beeps I described. This series of beeps had two beeps in rapid succession, followed by a longer pause, two beeps in rapid succession, longer pause. This repeated until a key was pressed. The owner has seen that occur only that one time, but she does not normally logoff while leaving the computer running.
We have uninstalled and reinstalled Office (including all the updates to make it current). We have verified that Bluetooth is not enabled, that the old Bluetooth pairings have been deleted, and that the batteries have been removed from the wireless keyboard and mouse. We have reset the PRAM and the SMC. We have run the Apple Hardware Test and it found nothing to report. We have disconnected and reconnected all of the cables (keyboard, mouse, printer, ethernet). The problem of the endless beeping after wakeup sometimes still occurs.
I imagine the next logical thing to try is to reinstall Mac OS. The owner is a bit reluctant to try that. She does have copies of her personal files on CDs, but she is reluctant to undertake reinstalling the applications. Reinstalling the OS without erasing the hard disk probably would be less disruptive, but is there much chance that would eliminate the beeping?  My guess is that something in the software somewhere has gotten messed up, and a completely clean installation would be the only way to guarantee to clear it up. Am I discounting the chances that just reinstalling the OS could fix it?
My feeling is that this is a software problem, not a flaky piece of hardware, but is that justified? If it might be a hardware problem, which part of the hardware might it be?
At one point, I had an idea that there is some software remnant of the wireless keyboard or mouse software still active that sometimes causes fake input that triggers the beeping. However, I don't know enough about the Mac to know whether that is a reasonably likely possibility, and, if it is, I don't know what to do about it.
All suggestions for clearing up this beeping problem will be accepted gratefully.  Suggestions of other experiments to try also are welcome.
If we do decide to try a clean install of everything, should I first install the OS from the original discs that came with the computer, then upgrade using the OS 10.6 discs, or should I just start with the OS 10.6 discs?

Answer 1

Hello, excellent work so far!
It doesn't sound like this much, but including for pondering...
The following table lists the new tones and their meaning:
Tone(s)          Description
1 tone, a 5-second pause, repeat          No RAM installed
3 successive tones, a 5-second pause, 3 successive tones          RAM does not pass data integrity check
1 long tone when holding down the power button          Firmware upgrade in process. See About firmware updates for Intel-based Macs for more details.
3 long tones, 3 short tones, 3 long tones          Firmware restoration from CD in process. See About the Firmware Restoration CD (Intel-based Macs) for more details.
http://support.apple.com/kb/HT2538
Can you count the beeps or flashes?
1 beep = no RAM installed
2 beeps = incompatible RAM types
3 beeps = no good banks
4 beeps = no good boot images in the boot ROM (and/or bad sys config block)
5 beeps = processor is not usable
In addition to the beeps, on some computers the power LED will flash a corresponding number of times plus one. The LED will repeat the sequence after approximately a 5-second pause. The tones are only played once.
Note: In this case, a flash is considered to be 1/4 second or 250 ms or greater in length.
It sounds more like some Hardware issue at the moment, but only by a slight margin.
One way to test is to Safe Boot from the HD, (holding Shift key down at bootup), run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions, Test for problem in Safe Mode...
PS. Safe boot may stay on the gray radian for a long time, let it go, it's trying to repair the Hard Drive
Reboot, test again.
If it only does it in Regular Boot, then it could be some hardware problem like Video card, (Quartz is turned off in Safe Mode), or Airport, or some USB or Firewire device, or 3rd party add-on, Check System Preferences>Accounts>Login Items window to see if it or something relevant is listed.
Check the System Preferences>Other Row, for 3rd party Pref Panes.
Also look in these if they exist, some are invisible...
/private/var/run/StartupItems
/Library/StartupItems
/System/Library/StartupItems
/System/Library/LaunchDaemons
/Library/LaunchDaemons