I picked up a few back issues on my last trip to the comic shop, and among them was a Superman annual from the '90s. Near the back ran an in-house ad for DC's then upcoming sci-fi imprint, "Helix". As we can see from the above image, Helix was actually the second choice for a name, as the previous one apparently met with some resistance.
If I remember correctly, the original announced name for the line was "Matrix", which obviously evokes some other imagery in lieu of the seminal movie of the same name. The movie series started in 1999 ("I know kung-fu") and the Superman annual was printed in 1996. Both DC Comics and the Matrix are housed under the Warner Bros. parent company, so you'd have to believe that someone from one branch informed someone from the other of the name, but we're talking about three or four years, here. Would it have been that big of a deal?
As it turns out, it wouldn't have mattered anyway, because the imprint died out in 1998 after a few short months of publication (a few titles were carried over into the Vertigo imprint, such as Transmetropolitan). So all of that hand-wriging was for nothing. There were, however, some fairly big names attached to some projects (Tim Truman, Garth Ennis, Tommy Lee Edwards, Howard Chaykin), and I seem to vaguely remember the character Cyberella...but then again, I may just be thinking about Striperella, who was a somewhat different character. Oh well.