Restoring lost settings.

When you say you've updated FFP, do you mean that you went to this site in a browser, downloaded the new version installer, and ran it to install the new version over the old, or do you mean that the Firefox automatic update system told you that there was an update available, and installed it for you?

If it is the latter, then I'm afraid that due to a bug introduced a few versions ago in the Firefox upstream code, the automatic updates are currently effectively broken with regards to the portable edition of Firefox.

I know that one symptom of the breakage is that the Firefox update overwrites various registry settings and effectively becomes the main 'installed' version on the PC where you run the up, and I suspect that it could also be that this causes it to use it's normal place to store a profile. The actual effect that you are seeing in your post is that FFP is not looking in the correct place for your profile data.

To fix it, if that is what happened, I would suggest that you download the current FFP version from this site - https://portableapps.com/apps/internet/firefox_portable make sure that firefox is closed - all versions, and install the download over the top of the current FFP. So far as I know, that should make it look at the profile directory on your flash drive.

that shouldnt happen.
Did you use the ini to change your folder layout or do you have the standard folder layout?

One way to do this is to copy your profile to a firefox browser located on your hardrive and use this full-blown back-up utility for firefox: https://addons.mozilla.org/en-US/firefox/addon/2109
then go to tools>febe>preform backup.
after its done go to your portable firefox and under file>open file
and find the directory where you backed up your profile and open it.
(If errors occur troubleshooting guides will pop-up from your browser)
This is what I do to sync my home browser and my portable one. I think it should work with your problem though I'm not 100% sure and remember to backup profile for the browser on the hardrive if you want to retain some files.

Be sure you are doubleclicking on FirefoxPortable.exe and not in /App/firefox/firefox.exe and that all your stuff are in data/settings.

Also be sure that local installed Firefox is not running when you are running your portable one.

A slight amplification on the other answers:

Firefox settings are stored in FirefoxPortable\Data\profile -- it shouldn't be hard to use My Computer (Windows Explorer) to hunt around on the removable drive and find that folder. It is relatively easy to make a backup of that folder by copying the whole thing to a safe place, or use the PAM backup function.

If you do a clean install of the latest FirefoxPortable, restore the profile folder to the same place, and start FirefoxPortable, your settings should be back. (By "clean install" I mean that you first delete FirefoxPortable and all its subdirectories, after making a backup of just the profile folder.)

Recent Firefox automatic updates seem to break Firefox portable. The solution is to not do the automatic update, but rather wait a few days for John to publish the updated installer for FFP. The new installer should update your Portable without messing with settings or losing track of where your profile is.