I admit I've never seen an actual interview, but if it's an Internet legend, it's a persistent one. On the IMDB "Alternate Versions" listing, it mentions that he prefers the shorter version, but as always that's grain-of-salt information (although that entry has been there for years). So I honestly don't know, I guess. Either way, though, there are some fans who do prefer the 99-minute cut, so I wish they'd include both. (Personally, I haven't seen either in quite some time, so I'm not sure which one I prefer, but I'm always interested in alternate released cuts).
I once asked Jackson via a post on the unfortunately now long-defunct "The Bastards Have Landed" website which cut he preferred, and he basically said something along the lines of he felt the short version would be better for general audiences, but the uncut version would be better for big fans of the film. He also mentioned that there was an even longer cut with about 10 additional minutes over the "uncut version" that he hoped to release as a special edition some day. My read of Jackson's opinion of the short cut based on that exchange is that he thought Miramax did a good job cutting it down to make it more palatable to general audiences, but not that he specifically preferred that cut. I wish that website hadn't disappeared, Jackson used to post there all the time and it was great having him respond to my question re: which version of HC
he preferred, even if he did kind of skirt the question by essentially endorsing both cuts (and his mention of an even longer cut makes me wonder if that one will ever actually surface one of these days). Vincent