Namely:
HKEY_LOCAL_MACHINE\SOFTWARE\Skype\Phone (which is empty)
HKEY_CURRENT_USER\SOFTWARE\Skype\Phone
The latter can be manually deleted, and Skype Portable then only re-creates it when it runs.
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Is this during one of the crashes? Are you relaunching? Please tell me you didn't kill the launcher process. Also, PLEASE post more details with bug reports (install location, Windows version, exact error, etc). I don't see this on my machine (possibly due to Win7 vs XP) and HKCU\Software\Skype is specifically cleaned up by the launcher on Skype's exit.
Sometimes, the impossible can become possible, if you're awesome!
This happens during normal launches. There aren't any errors. It's XP SP2 and the install location is %homepath%\My Documents\SkypePortable
It's commercial software.
One thing I noticed lately is the updater (skype) now works with the portable version, but it still updates it to the start menu.