Firefox's updater has a bug where a portable or secondary install of Firefox will overwrite the locally installed Firefox's registry settings when version update is performed. It appears this bug was introduced within the last few point releases of Firefox 2.x. It's filed as Bug 406335 within Bugzilla. Please vote for this bug if you have a Bugzilla account.
What Goes Wrong
When you auto-update a portable or secondary install, the auto-updater treats it as an actual install and updates the local PC's registry keys to point to the portable or secondary install as the currently installed version of Firefox.
What you should do
Either avoid auto-updating and download a new version of Firefox Portable for each version or allow Firefox Portable to update before allowing your local version to update (the portable version would steal the registry settings and the local one would steal them back in this case). You can also re-install the local version to fix this issue.
And, before anyone asks: no, we can't set updating to disabled by default.