I'd first like to thank you for making these apps portable. I'm working on some projects with USB drives and this comes in very handily. I'll post more about my projects soon.
Now for the issues...
Why isn't PFF1.5 executables and dll's compressed? I compressed them myself and shrunk it down about 40%. Less USB access = faster startup 
Also, I have my profile and other personal settings in a seperate directory. It took me a while, but I figured out that I had to move the PortableFirefox.ini to the same location as PortableFirefox.exe and for the ProfileDirectory setting, I had to use "..\personal\FFProfile" to specify the directory which contains my profile.
This issue happens with Portable Thunderbird too, but not with Portable GAIM. With GAIM, I can leave the ini file where it is and use \personal\GAIMSettings to specify my account information. Is this fixable?
I'd also like to recommend myEasySynch. I use it at work to synchronize a utility folder with multiple flash drives for our support department.
It's just a single file and doesn't use the registry.
Again, thanks for all your efforts.
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as for UPX
FF 1.5 cannot be UPXed because it will break it's new auto-update feature
Embrace your dreams
A quick search of the forums would reveal this has been answered at least 6 times already. It's a matter of auto-update vs 8mb. Auto-update won on both FF and TB 1.5.
As for the INIs, they HAVE to be in the same directory as the EXE or one of the other mentioned directories. This is explained in detail in the readme.txt within PortableFirefoxCode, etc.
Sometimes, the impossible can become possible, if you're awesome!
I just wanted to share this, hoping it might be usefull:
I run Portable FF from a folder on my work machine where I have no admin priviledges.
I tried UPX (version 2.0 27 Apr 2006 see http://upx.sourceforge.net/) with the following command lines in the \firefox and \components dirs:
upx *.exe --best --compress-icons=0 --nrv2d --crp-ms=999999 -k
upx *.dll --best --compress-icons=0 --nrv2d --crp-ms=999999 -k
This STOPPED PFF from working. After eventually restoring the files I tried:
upx *.exe
upx *.dll
in ther same dirs. This brought the firefox dir from 9.24 Mb to 4.33 Mb. PFF works perfectly and as of now hasn't shown any problem.
I eventually did autoupdate and it worked successfully from 1.5.0.1 to 1.5.0.3 (extensions included).
The problem is just that filesize goes back to the original about 9 Megs. So at least you are in lack of space, doing upx *.exe and upx *.dll again will work.
Or though this worked for me, I reccomend using the -k option or to backing up the dirs before testing.
Cheers
Lo