MacBook Pro won't sleep or stay shut down?

Product: MacBook Pro 13" "mid 2009," 8GB RAM (3rd party RAM upgrade), 2.26GHz, Mountain Lion 10.8.2
This happens ~75% of the time:
1) When I put it to sleep, the fans keep running, hard drive keeps spinning, and the outside front pulsing light goes through unusual on/off pulsing cycles. When I open the lid, it's at the login window. So it knows I put it to sleep, but it doesn't stay asleep. And I can't just put it to sleep and throw it in a bag -- it would overheat.
2) When I shut down, it goes through the process, and as soon as it's off, the front pulsing light turns on, and the computer starts up again. I can't stop that from happening. So to shut down fully (for travel, unplugging power, etc), I need to force shut down (hold power button for several seconds), and that can't be good to do so many times.
I've read through so many posts online (not a totally unique issue here, Apple!), and I have done all of this:
- archive and install
- clear all faulty fonts
- reset SMC
- reset PRAM
- removed all strange startup items (with Genius Bar guy)
- delete /Library/Preferences/SystemConfiguration/com.apple.PowerManagement.plist and /Library/Preferences/SystemConfiguration/com.apple.AutoWake.plist to re-create them
- remove all sharing (file, printers, iTunes library)
- turned off Bluetooth
I even did a clean install, then pulled in my stuff backed up on external HD. Unfortunately I didn't test enough if I could replicate these issues before restoring all my files and settings.
Apple Genius Bar told me that it's not a hardware issue -- that's all been checked.
Anything else to do? other than doing another clean install and copying files, applications, etc. one by one? (which might not fix anything)
Thanks so much for any help.

I don't have any good solutions as it seem you have tried all the advised repairs and resets. If it were me I would wipe the HDD clean and install 10.5 or 10.6 depending on the installation disks you possess. If the problem is resolved then upgrade to 10.7 or 10.8 and see what happens.
I have a MacBook Pro that would not work correctly with an interim OS update no matter how I approached it. The consensus on this forum was that I was doing something wrong. I reinstalled to the pre update state and waited till the next upgrade was released. When I applied this everything was fine and has remained so. Perhaps OS X 10.8.3 will offer you some relief.

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