I recently lost my USB drive and had to start from scratch. I had been using Chromium Portable for a long time and was happy with it.
After the crash I was wanting to get back up and running fairly quickly so I tried out Maxthon. It didn't work well with KeePass (issues with window focus) so I downloaded Google Chrome Portable and went with that.
I had been using it for a couple of weeks until yesterday when I started it up and noticed it appeared to be reset to defaults and my bookmarks were gone.
The last time I shut it down was the night before and I had shutdown my PC right after. I was using RunLocally=true so I just figured I shut down before it finished copying my profile back to USB. I restored my profile from backup and went back to using it.
I shut it down yesterday afternoon and when I started it up about 30 minutes later, again it appeared to be back to default settings, my extensions were gone (the directory was actually empty), as were my bookmarks.
So I completely reinstalled Chrome from scratch and restored my profile from backup again. I set RunLocally=false thinking it was something with copying my profile back and forth to HDD.
I shut it down after restoring my settings and started it back up - my extensions were gone, all settings were at default, but this time my bookmarks were still there. I checked the GoogleChromePortable Data folder on my USB and the extensions directory was indeed empty.
It appears Chrome is erasing my settings and deleting my extensions when it shuts down.