Those aren't two interpretations of the same piece of news; if Game Informer are to be believed, then two fighting games are currently in development, both pitting the stars of Namco against the stars of Capcom
Capcom vs Namco will be done by Capcom within the Street Fighter IV Engine, while Namco vs Capcom will be done by Namco within the Tekken 6 engine. Yoshinori Ono will be heading Capcom's side while Namco Bandai's Katsuhiro Harada is expected to be in charge of the opposing project.
And now it's time for my two cents. After the on-stage shenanigans between Harada and Ono at EVO this past year this could be very true. Personally I'm at a bit of a lose for this one. When Ono was on stage teasing everyone to wait for Comic-Con for the announcement I was just running through all the games Capcom could be making... Darkstalkers 4, Rival Schools, TvC for PS3/360, SSFIVT, 3rd Strike HD Remix, and even Alpha 4 (which would have made me the happiest person alive). The thought of having Capcom vs. Namco actually disappoints me. Namco offers nothing of value to a fighter when it comes to the 2D realm of fighters. Sure we could see Kratos from ToS vs Ryu of Street Fighter but, I feel that would look all too weird. And with Marvel vs Capcom 3 in development, why announce/make another VS game when it will no doubt be overshadowed by Marvel 3.
I'll only say one thing for Namco vs Capcom. Street Fighter EX series.
http://kotaku.com/5591240/rumor-namco-vs-capcom-capcom-vs-namco-in-development