I have a friend who is a lesbian of Peruvian heritage. This woman has a potty mouth and is very politically incorrect. So she recently got into a relationship with a liberal woman with a lot of white guilt. My friend tells me she has to bite her tongue now because her girlfriend will scold her for making racist jokes. Her girlfriend does all the things like living in a poor neighborhood of Oakland and joining community groups out of guilt. So recently I was at a party where I met my friend's significant other for the first time. My friend with her foul-mouth started pouring on the Asian jokes at me all evening. So the next day she calls me up like she usual does to shoot the breeze and I asked her I thought you had to bite your tongue around your girlfriend because she doesn't like racist jokes. She tells me that's only for blacks. She don't give a crap about Asians.
Well the fact is the protectors of Star Trek are not going to admit it was a very basic and racist stereotype to begin with. The fact that they don't bring up the obvious Chinese associations with Klingons in the original series shows that. The Klingons were at the start the stereotype of Western enemies that only thought of war and conquering without reason except for their own enrichment. There was nothing of actually identifying Star Trek aliens with actual human ethnic cultures until TNG. People feared the Chinese back then and they do even to this day and you hear the same accusations of motive. All the alien invasion movies of the 50s and 60s were all about getting people afraid of communism. The movies that were about aliens taking over the bodies of loved ones were getting people afraid of communist recruitment at home. That's why even in Star Trek Chinese elements were used to represent communism because that was a tradition part of Hollywood propaganda to depict those who should be feared. It wasn't even really communism that was depicted. The angle of using the Chinese/Asians to represent these things is older and certainly not extinct.
I remember watching this movie on the Sci-fi channel. I forget the title but it was about a huge alien object hovering over Tibet. Of course the Westerners were seeking enlightenment and wanted to make contact. The Chinese however could only think of destroying it. It was a horrible science fiction regardless of the stereotypes but they made a sequel anyway but this time the alien object was hovering over I think was Israel this time. Good, no Chinese to vilify which what I thought until the very end where out of no where with no rhyme or reason China sent Flankers on a one way suicide mission across Asia to destroy the alien object.
It certainly doesn't surprise me in this contradiction with Gene Rodenberry's vision of Star Trek and the perpetuating of stereotypes. Does it mean Gene Roddenberry is racist? No. That's just a sign of the times he was living in despite he would have been considered a progressive back then. Today I know people who think of themselves as liberals yet they only are "kind" to people of African descent. I have another friend when he was attending San Diego State rented a room from a African-American police officer who was married to a hot blond. He told me the guy's wife had a contentious relation with her father for marrying a black man. But here's the thing... she hated Asians as much as her father didn't like blacks. If you live in a binary world like the NOMAD probe, that does not compute and that's why NOMAD self-destructed.
I think the movie you are talking about is the Epoch (2001).
And its sequel is called Epoch Evolution (2003).
Star Trek has always been about politics. And mirror the real world in some ways both socially and politically. The Star Trek movie The Undiscoverd Country (1991) was about the beginning of peace between the Federation and the Klingons just as the cold war came to an end. And in the 3 90's series where the Klingon empire has become a shadow of its formers self and the Federation is all dominent in the Alpha quadrant. The series began to explore both the Delta Quadrant (Voyager) and the Gamma quadrant (Deep Space Nine). And of course spreading Federation (human values) to the Gamma and Delta quadrant locals. This mirrors the unbridled optimism of that era where the stars are the limits.
For me this is how i see the race/political divisions on Star Trek
Federation = America/Allies
Klingons = Soviets/Russians
Romulans = Chinese/Asians
Cardassians = Rogue/Middle East states