I recently had a similar issue, Firefox doesn't register itself correctly as the default browser. Or more precisely: Some browsers (i.e. MyIE2) have an unusual way of registering themselves, and Firefox can't cope with that. Be sure your registry keys basically (I removed some stuff) look like this:
[HKEY_CLASSES_ROOThttp]
@="URL:HTTP (HyperText Transfer-Protokoll)"
[HKEY_CLASSES_ROOThttpDefaultIcon]
@="D:PROGRA~1MOZILL~2FIREFOX.EXE,1"
[HKEY_CLASSES_ROOThttpshell]
[HKEY_CLASSES_ROOThttpshellopen]
[HKEY_CLASSES_ROOThttpshellopencommand]
@="D:PROGRA~1MOZILL~2FIREFOX.EXE -url "%1""
It's important that the default keys unter "httpshell" and "httpshellopen" are empty! Same goes for the "https" protocol.