Update: After further investigation, I found is the problem is in google-chrome application not in Chromium-browser. My Mistake!
Dietrich Ayala brought this problem to my attention. For some reason google-chrome browser constantly makes itself the default browser on Ubuntu 10.10 and later versions. This is annoying when you are testing Firefox Nightly Ubuntu builds. You can choose to remove the google-chrome, but that is not a solution.
First, I tried to reproduce this problem on multiple Ubuntu machines. To reproduce this problem, installed Firefox nightly using Firefox Nightly PPA. Remove any other browsers expect google-chrome.
It took very long time to find the solution to this problem. The chromium-browser package adds /usr/local/share/applications/mimeinfo.cache which supersedes the default system application settings. The solution is edit this file and make it read-only using chattr command.
$ sudo nano /usr/local/share/applications/mimeinfo.cache [MIME Cache] application/earthviewer=google-earth.desktop; application/keyhole=google-earth.desktop; application/vnd.google-earth.kml+xml=google-earth.desktop; application/vnd.google-earth.kmz=google-earth.desktop; application/xhtml_xml=google-chrome.desktop; text/html=google-chrome.desktop; text/xml=google-chrome.desktop; x-scheme-handler/ftp=google-chrome.desktop; x-scheme-handler/http=google-chrome.desktop; x-scheme-handler/https=google-chrome.desktop; #Remove all the google-chrome entries, like this. [MIME Cache] application/earthviewer=google-earth.desktop; application/keyhole=google-earth.desktop; application/vnd.google-earth.kml+xml=google-earth.desktop; application/vnd.google-earth.kmz=google-earth.desktop; # Make it read-only even for super-user sudo chattr +i /usr/local/share/applications/mimeinfo.cache
After making these changes. Open Firefox Nightly and make it the default browser. Now this system setting will remain unchanged.