When doing an update using Firefox's internal updater running within Firefox Portable, the FirefoxPortable.exe launcher does not properly remain running through the update and the app's close after the update. This can result in some empty directories and registry keys left behind on the local machine.
PortableApps.com Platform users that update via the platform's internal updater and users who manually download each release to update are unaffected by this issue.
This issue is fixed in Firefox Portable Nightly 61 which is currently mirroring for download. This bug will remain open for tracking until updated through the stable channel.