Have to say that this is quite unfortunate. Cant imagine that many people will install both on their system to make sure that they can decode both versions. Also if it is true that pkzip havent published the changes then the likelyhood is that other zip apps will go along with the winzip version.
Considering to the masses WinZip is almost synonimous with ZIP files now, I think WinZip will very likely become the standard. The same way Word is synonimous to a word processed document.