Error Saving Preferences on exiting Mail Preferences

Hi, I am getting the Error Saving Preferences error on exiting Mail Preferences with advice to check disk space and directory permissions on ~/Library/Preferences. Not knowing what the official permissions should be I booted the iMac from the Leopard installation disk and in Disk Utility I repaired file permissions but this did not make any difference. I have followed other instructions I found in Apple Discussions which were for a previous OSX where I backed up the Mail directory and then moved ~/System/Preferences/com.apple.mail.plist to the Desktop. Per instructions I then fired up Mail which picked up my Mac account straight away but again on exiting Preferences without even adding any new mailboxes the same error cropped up... in fact I don't think a new plist was created. I returned the old plist and Mail directory.
It may be worth mentioning that just before this problem cropped up I had been trouble-shooting another problem where every minute my active window would lose focus, I tracked this down to HP_scheduler (I have an HP all-in-one printer, C6180) and on killing the process the problem went away, but I think it was also a symptom of the real cause which is still unknown as the printer software has been installed for about a year, last update was months ago... but before I had tracked the issue down to this I had use MacScan2 to flush just my Safari caches and temporary files etc, it was running in authenticated mode, may mean something, may not. Subsequently to discovering HP Scheduler was to blame I uninstalled all the printer software using the HP uninstall package.
Around this time a third problem transpired where settings were not being retained in various System Preferences. Unfortunately I didn't pick up on it straight away as being a third problem and now can't remember whether it started before the window lost focus problem or not. The first time it happened was when I tried to put MacScan2 into the startup list for my login, it could be added but on checking the addition it wasn't retained in the list and well I thought nothing more of it as it was the first time I had tried to do such a thing. Then I noticed the Mail issue just by chance and subsequently, through seeing someone else's problems logged back in 2006 I think, I noticed that although I could change screensaver I could not make a change in desktop photo stick.
I have since reinstalled the printer software and I am no longer losing focus from the active window.
However, I think it is probably the case that the Mail Preferences, Startup Items and Desktop Preferences issues are all the symptoms of one and the same problem and I would be very grateful if anyone is familiar with and/or knows of a solution to this issue.
Many thanks for reading!

Well, in the end I tried many things including lots of things that I thought wouldn't help such as cleaning out caches, running crons; I was using IceClean and pretty much tried every system maintenance option but to no avail. I have removed MacScan and have kept Norton, which this time found a few things in my .wine folder, but I have only performed a few full system scans as it takes a full day.
This resulted in the knowledge that I would have to do a Leopard reinstall if that failed then a complete restore from TimeMachine which I knew would take ages, but fortunately the reinstall worked perfectly and effortlessly to solve the problem, and it only took 30 mins to update the security patches including 2 automatic restarts.
Phew!

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    There’s a discussion about the very same problem I’m having at <http://discussions.apple.com/thread.jspa?messageID=2047886&#2047886> about Mail not being able to save preferences... or at least a message pops up each time despite the fact that the preferences are saved. Annoying, really. I’ve followed all the steps suggested in the above thread, including terminal commands and repairing of permissions. However, the problem didn’t go away. Unfortunately, the thread above was closed (without being answered), so I had to open a new post. Here’s a description of the problem as stated in the above thread... and the problem occurs exactly like that on my Powerbook running 10.4.7.
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    Can somebody help me with those 2 problems ?
    Best regards.

    If you are right with the second option that it does not affect what is deleted from my computer, I would be left with only 7 days of deleted messages on the server, not for a month or 2 as I want.  But that could do it, since the need to access deleted emails concerns mostly new deleted messages and because all deleted messages would still be on my computer.   But I doubt that I is possible.
    Yes, you have to check it with your mail server. I can only tell you what I observed in my accounts.
    The manual is rather ambiguous:
    Delete a message
    Move the pointer over the message header in the preview, and then click the Delete icon that appears. Or select a message in the list, and then click the Delete icon in the Mail toolbar.
    Deleted messages remain in the Trash mailbox on your Mac or on the mail server until they are permanently erased. Messages that are deleted from mailboxes you created on your Mac are moved to the On My Mac mailbox, located in the Trash mailbox.
    HideSet where to store deleted messages
    Choose Mail > Preferences, click Accounts, and then select an account. Click Mailbox Behaviors and in the Trash section, select where you want to store deleted messages until they are permanently erased.
    If you deselect all options for an account, deleted messages remain in their original location and are shown dimmed or are hidden. To show or hide deleted messages, choose View > Show Deleted Messages or View > Hide Deleted Messages.
    ShowPermanently erase messages
    You can retrieve deleted messages if you haven’t emptied your Trash mailbox or rebuilt your mailbox since deleting the messages, or if Mail hasn’t permanently erased the deleted messages. Just drag the deleted messages to another mailbox.

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