[spoiler] It was AVG's fault [/spoiler]
This is less a bug/problem report, and more a message in a bottle to anyone else that might have the same problem. (and I apologise for rambling nature of this post)
I've got Google Chrome Portable (and a few other PA programs) on a computer (XP Home, SP3) I don't use often so it took a while for me to do anything investigation/thinking about it.
For a while now, ever time Google Chrome was updated on that computer (I download the paf.exe plus the chrome_installer.exe and do a 'offline' install :-)), Google Chrome 'lost' all extensions and acted like it was a local install (note: PortableApps is definitely NOT installed to a 'Program File' folder).
No other portable programs installed (not even Iron Portable) was affected.
I would then remove Google Chrome Portable, re-install it + the extensions, and it would be fine until the next time I got around to updating Google Chrome Portable.
Long story short, it looks like AVG (Free, 2013) was reacting to the update and a lot of stuff would go missing from Google Chrome Portable's Profile folder.
That no-one else seems to of complained/reported the same problem (to the best of my searching ability) suggests it's a rare problem, and maybe just me?
One thing I do (on that and other computers) that might be a bit different, and perhaps maybe a factor in causing the problem, is that I use the SUBST command to turn the folder PortableApps is installed into to a virtual drive to make updating & stuff easier
(eg: turn C:\Downloads\PA into V:\ )
I suspect that running PortableApps (and Google Chrome Portable) on a virtual drive + doing a 'offline' update of Google Chrome Portable + AVG Free 2013 = the cause of this problem.
Unfortunately, due to replacing AVG on that computer with a different anti-virus, I'm not in a position to check if using the automatic updater results AVG (Free 2013) doing the same things to the Google Chrome Portable's Profile folder, or if running it in a SUBST virtual drive was a factor.
So ..... sorry about the long post about a problem I'm no longer having, but if someone is having the same (or similar) problem hopefully this might help