There is a way around this though. Your copy of Firefox Portable should have a file named FirefoxPortable.ini in it’s directory. If you don’t see that file, it may be located in the Other/Source folder. If it is, you will simply need to copy it back to the root directory where the Firefox Portable executable is located. Once it is there, you will need to open it with a text editor and change a single value inside:

Locate the following line:

AllowMultipleInstances=false

And change it to:

AllowMultipleInstances=true

That’s it! Next time you try to open Portable Firefox it won’t be checking for a running instance and will happily coexist with an installed copy.

Zdroj: http://www.terminally-incoherent.com/blog/2009/06/11/running-firefox-and-firefox-portable-at-the-same-time/