well, here some counter questions for you theorizers
1. it would be easy for hudson to give a proper statement on that matter. so why they can't?
2. what makes more sense: 1. hudson did this 2nd run to bestow all those people a copy of sapphire for a reasonable price, which missed out the 1st print back in '95? or 2. some clever fellows duplicated it to flood the market with pirate-copies and make big cash in the first period (until the world get noticed)?
3. why trader 2 put that specific "copy" into their show case of "proven counterfeits" to prevent people of buing it?
4. why you can't find that specific "copy" in any regular retro-stores in akiba offered nowadays, but a lot of the old "original" ones? if it's proven a legit 2nd run, then why stores don't offering it if they where such widely spreaded back in 1999/2000 all over japan (as some of the people all the time argue)? I never have seen one in the last several years, in contrary on ebay etc. you could find hunderts of them in the same time span!
5. back then, around when the said copy where released, absolutely nobody got noticed, that those coming from a legit source (e.g. hudson), nor was it publicized in any magazines or public media. so there never was an offical release of it, which is very untypical in japan. why?
6. and, who exactly ever sent a copy of that 2nd run to hudson to clarify it, and got the answer that hudson couldn't find anything wong with it?
i've readed this so many times on ebay auctions and when i asked the seller about that matter, he couldn't give me a proper answer for that. therefore i think, this is just an invented story made up by some guys who wanted to sell saphhires still for a good price (or not to get banned by ebay), after the world got noticed about those pirates once.
so there are a lot of arguments which speaking for a counterfeit, but very small evidence for a legit 2nd run from hudson soft.