I'm unsure what caused this, or even if I could reproduce it, but here we go.
I have FFP 3 in X:\PortableApps\FirefoxPortable and FFP 220.127.116.11 in X:\PortableApps\FirefoxPortableBackup. I downloaded the 18.104.22.168 installer to update my backup (which is currently being used until all of my plugins are updated) and told the installer to install to X:\PortableApps\FirefoxPortableBackup. When I restarted FFP 2, it was still at version 22.214.171.124. I tried this again but had the same problem. I then tried using my FFP 3 install and it immediately crashed (which makes me think it still tried to install over the default X:\PortableApps\FirefoxPortable path. After I deleted the FFP 3 install, and renamed my backup to the normal path, the upgrade worked without any problems. Just an observation.