Very well could have been... hard to ID a fast moving spec, or even estimate altitude. The only thing that makes me think otherwise is just how rare SR71 flights likely were in the late 90s.
Amazing that a plane developed like the SR-71, which required advancements in the then current technologies to work, has characteristics that are still up there with "cutting edge" developments.
The Buff, the SR-71 and the Warthog remain some of the "premiere cutting edge air-frames" ever put out for performing their intended tasks as far as I'm concerned.