Using LaunchpadCleaner (LPC) -- which has a really sucky interface and very limited control over your LaunchPad really -- I was able to at ~LEAST~ know how OS X Lion was going to mess around with the icons... so with a combination of sheer GUESSING, LUCK and a terrible app UI, I was able to at least somewhat predict the outcome of swapping around icons in LaunchPad when it goes quirky.
For the sake of the argument beolow, let's call OS X's arrangement the SCREWY arrangement here, and what you actually see in LaunchPad as it is (before restarting and OS X scewing it up) the "LaunchPad" arrangement.
In LPC it shows me EXACTLY how OS X is going to move around my icons. In one case, I had two folders that were next to each other and kept switching places with each other. Incidentally, when I switched them to 'match' what OS X's screwy arrangement, they followed the intended arrangement that I wanted to see in the LaunchPad arrangement!!
So from there it was hit-n-miss. With the ~help~ of LPC, which has the ability to refresh the Launchpad itself and view the Screwy arrangement, I was dragging icons around, placing them in folders, removing them from the folders, until I ~FINALLY~ got pretty much the arrangement I wanted (without having to resort to a full-revert of the Launchpad... which is what I did awhile back and OBVIOUSLY everything still gets screwed up eventually).
The thing is... SOMETHING is causing LaunchPad to get screwed up. Here are my suspicions:
• Sophos Antivirus
• DropCopy
• Cocktail (via resetting permissions)
Sophos has screwed with me before (the version I'm using is the latest) when it totally messed up versioning and auto-save on Lion (and corrupted the original files too -- how nice). It might be screwing with me again.
DropCopy? Not sure, but I accidentally fired it up at the time I noticed the strange Launchpad behaviour.
Cocktail coz I was repairing permissions while arranging stuff in the Applications folder.
I think it was the arranging stuff in my apps folder that might have done it for me -- I started categorising my apps and putting them into folders. That's when the Launchpad started getting quirky -- with my added suspicions coming from those apps above.
If anyone can cross-check their Launchpad behaviour with these apps (do you HAVE any of these apps) and the act of moving stuff around in your Applications folder, perhaps we can draw our own conclusions on WHY Launcpad is acting up this way.
Then we can advise people what NOT to do...