Hi there... sorry for the delay in posting what happened – I've been trying a few other things.
Okay, the long and the short of it is that Apple didn't have an answer. It was referred to an Apple engineer by the senior technician, but they came back after a week with queries over a couple of files in my plist folder. These were indeed causing problems, but seem to be an unrelated issue.
I pointed out that the problem always happens after exactly 4 hours, which is when autoshutoff comes into effect. Looking at my wife's Macbook, which is running Snow Leopard, there is no autoshutoff in there.
Having spent a long time looking into this, I decided to turn autoshutoff OFF (0), and it's cured the issue entirely. This leaves the hibernate mode alone (and in the same state as it is on the wife's SL MB).
First of all, open Terminal (in utilities) and type pmset -g
This shows you your power management settings. It's different depending on whether you have your power supply plugged in or not.
In terminal, enter
sudo pmset -c autopoweroff 0
This will give you this message:
"WARNING: Improper use of the sudo command could lead to data loss
or the deletion of important system files. Please double-check your
typing when using sudo. Type "man sudo" for more information.
To proceed, enter your password, or type Ctrl-C to abort."
Type your admin password, then press enter. If you want to check that it's taken, enter pmset -g into terminal.
You'll need the power supply plugged in to see the change. The -c in the command used means this setting only relates to the power supply. I'm going to try it with -a too, which will also relate to the battery. (-b would be battery only). If you wanted to turn autopoweroff back ON, you'd put a 1 at the end, instead of a 0.
I'm going to try -a tonight, as I have one issue now where if I unplug the sleeping laptop from AC, it enters a dark wake, and is unresponsive for 20-30 seconds, with a black screen. However, the settings I've changed mean I no longer get the huge list of errors in Console after a wake, or if I look at the sleep log with pmset -g log
I've got one more thing to try, before I get back to the technician delaing with my request. Once I've narrowed everything down to this, I want to ask what autopoweroff really does!
Hope this helps... It's great for me to have my machine running correctly again. Unfortuntately Apple did seem to indicate that they'd not come across this problem before, which seems unlikely, but they did say they thought it was an issue with files migrated from an old OS. Did any of you with this issue do 100% clean installs, and not migrate anything? The issue definitely seems to have happened when I installed the update, but I wouldn't be able to say for certain.
Please do post how you get on...