Odd. Maybe it was theater-only until the Mewtwo Returns DVD came out? I know the Birth of Mewtwo CD Drama was distributed around that time, so perhaps that could be the reason why the ten minutes weren't on the video. Though I hear they did upgrade some of the animation when it was released on video or something like that. The doors opening weren't CGI when it was first released in theaters.
*insert Jeopardy music here*
Okay, looking it up on Bulbapedia, it suggests that in the VHS release, the ten minute origin wasn't included until it was released on DVD. And the whole CGI was done to the American release. Everything's still all hand-drawn in the original Japanese.
So yeah, you have a normal copy. I don't know why they did that, but hey.
That's a pretty good explanation of the different versions of the First Movie. The 4Kids dub of the first movie was based on this special edition, and the whole thing was dubbed. The "Birth of Mewtwo" stuff was removed from the US theatrical version at some point - whether it was always the intention to take it out of the movie or taken out after it was dubbed is unknown. Since Warner Bros. had a heavy hand in influencing the dub of the movie, it's not really known whether it was a decision by 4Kids or WB, although it was likely to increase the pace of the movie. (seeing as Ash takes about 15 minutes to appear in the movie if the "Birth of Mewtwo" stuff is left in)