Sync problem: Unchecked items stay on Touch!

When I sync, only checked items do sync, but unckecked items that were previously checked or items removed from checked playlist aren't deleted from the iPod Touch!
It's like it only goes one way! Checked items go in the iPod Touch, but changes that should remove items FROM the Touch stay there!
I use AutoSync because it's much easier than manual (for me, at least), and it used to work perfectly.
I can't pinpoint exactly when it started to go wrong on my iPod Touch, maybe it NEVER worked... How can I not be sure? Because I don't sync it often, I use my iPod classic a whole lot more for music, and only started recently putting more music & video on the Touch.
Now it really bothers me to have Christmas music on it that I can't seem to remove (soon it will be OK though...) ;o)
So, I use Auto-Sync, and checked "only sync checked items"... but it doesn't work!
I now upgraded to iTunes 9 and iPod Touch OS 3.1.1 and it's the same...
The weird thing is, under iPod Touch in the left pane, the changes I made in the playlist/videos and such are all reflected! I thought it had worked until I looked on the Touch...
iTunes left pane under "iPod Touch": No more Christmas music (but new music from the MBP), no more podcasts, different videos.
I turn on the Touch... No changes! :
The music that shouldn't be there IS, the podcasts are still there...
But it added the new content.
So why does the left pane reflect the changes and not the reality?
Why does the Touch not sync right?
I always thought the iPod (whatever it's type) while in auto-sync, would just take in what's on iTunes and copy it (or update it), and if one track wasn't on the iTunes playlist, you'd lose it (which, before, was scaring me)...
And it's not doing that properly?!
*This also happens in the pictures & app departments:
I removed some pics (unchecked some lists/events in iPhoto tab) but they ALL are on the Touch.
And when I unchecked an app in the apps tab, I got a popup window reminding me the app would be removed from the Touch if I synced, but it is still on the Touch.
Could someone please help me?
...P.S. I also notice syncing is taking forever... Which isn't new either.
Syncing takes about 2hrs for just 8G of content! (with very few changes in that content)

OK, this is WEIRD.
Before I posted the topic, I did a test : reset the iPod Touch, do another sync, check again...
It did NOT solve the problem, and the sync took just as long as the first one.
Well whaddayaknow?
Later in the evening, the unchecked items had disappeared from the Touch!!! (except the pictures... all iPhoto content is on the Touch... lucky I don't have a lot in there!).
Trying to remember what the heck I could've done in the meantime, the only thing I can remember is opening "music" and seeing the library being updated (or actualized?)... And going in the app store where a couple apps had to be updated.
...Could one of those things had done it?
The Touch went to sleep between a)11am when the problem was still there, after the sync and b) the evening when it was all good.
But I didn't do a reset or put it on "off".
So it's a mystery.
I know I'm not crazy, and I always am very careful to check everything before posting.
Now, if anyone has any idea about crazy syncing time... I'll post another thread for that. (8G of content on the Touch takes 2hrs to sync, while 60G of content on the Classic takes only 10 min!)
Thanks all anyways!

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