Myriad of issues (hibernation, microphone, power management, alsa)

Question

Hello!
I've had arch up and running beautifully on my Thinkpad T61 for around six months; everything up until this point worked well - audio, video, networking, internal microphone, etc. I'm currently running SLIM + XFCE4 + Compiz WM.  Very happy indeed!
On October 3rd I upgraded a number of packages; like a good archer I read over the list to make sure none were unneeded/would break anything.  After the update I shut down.  On October 4th, I ran an update again (I can't remember why) and updated some more packages; that finished.  I then closed my laptop lid to suspend it; that's when all hell broke loose.
At first I noticed that it wasn't suspending; I can tell by the lights on its lid.  I opened it up and saw that it was exactly where I left it.  I tried to suspend through the XFCE logout menu and noticed it was missing hibernate and suspend.  I thought; that's weird, let's reboot!
Upon reboot, an extremely loud "BEEP" began nonstop - I quickly switched TTYs, went into alsamixer, and tried muting everything. Eventually I found that if I completely lowered the volume on my microphone the beeping stopped.  That was weird. I rebooted; but the alsa settings were lost (though they were kept for everything else) on the microphone and the beeping returned.  I tried saving the alsa state (alsactl store) and saw that it was saving any changes I made to any channels other than the microphone. Annoying. So I just disabled the internal microphone in the BIOS, for now.
Back to my suspend issue: I knew that I had upgraded pm-utils; so I suspend from CLI to see if it would work. It did.  I then thought, it must be an ACPI issue - low and behold, checking the acpi log in real-time showed that the laptop lid wasn't being noticed, nor were my hotkeys.  I checked my handler.sh file, and yup - it had reverted to a non-T61 state. Very rude indeed. I then replaced it with the T61 handler.sh from the wiki, and suspend/hibernate worked again, hotkeys, lid closure, etc.   However, when resuming from suspend, he loud beeping returns - even though I've disabled microphone in the BIOS.
However, my hibernate/suspend options were still missing from my XFCE log out menu - I did some research on this; I made sure that I was a member of the power users group. I also tried logging in to XFCE as root - same issue.  I also noticed that my battery percentage/charging indicator has disappearance from the XFCE notification window; when I set the Power Management properties to "show when battery is detected" it remains hidden; if I set it to "always show" it just shows a power plug.
So I basically have three outstanding issues: My microphone is making a crazy beeping sound & alsa refuses to permanently mute it; suspend & hibernate are missing from XFCE menu (and the Power Management window has no affect - if I push the power button, it shuts down via acpid rather than prompting me as it should), and the battery indicator is missing.
Here is my latest pacman.log
Here is my messages.log
Here is my rc.conf
Any help would be much appreciated!  Thanks!
Yochai

Answer 1

I've had similar issues as well with the recent updates. Two things have helped but not completely eliminated all my issues. It should be noted that I'm on a T410 so this may or may not work for you. My kids X61 has had no issue whatsoever.
1) Removed hwclock from DAMONS in rc.conf - this fixed a gnome 3.2 issue.
2) Turned off wireless (hardware switch) before suspend - suspend now works - I don't really feel this is a fix but more on the lines of a workaround until a real solution is found. 
You may also want to look at some of the recent suspend threads people are finding different things on different models for the suspend issues at least.