Well the submarine patent argument is a bit of a strawman because it is equally valid for PATENTED software as well.
Look on MPEG-LA page where they state that licensing the patent from them doesn't guarentee against litigation by other parties.
Also cross reference the Alcatel-Lucent v. Microsoft case where AL sued Microsoft for mp3 patent infringement despite Microsoft already paying Thompson license fees.
Software patents are such a joke because no one is absolutely sure who own the patents to what exactly. It looks very much like a cartel managed by "legitimate businessmen" if you know what I mean