I’m pretty sure it’s plugin related. I don’t have Zemanta or other plugins mentioned in other posts that caused the same issues.
So, rather than disabling one plugin at a time, I found a work-around:
1. Deactivate ALL plugins
2. Re-arrange the layout to the one you want. If it’s plugin related like my case, this time the new layout WILL save.
3. Re-activate ALL plugins.
The drawback is that some plugins will require you to redo the settings again, but that’s worth the price for me. I don’t have to scroll a billions line down just to hit “Save Draft” now. Yay!