The "Menagerie" dvd I mentioned earlier shows a total running time of 99 minutes, so they've been chopped too, though all the dates show 1999. I'm not sure where the cuts are, because I'm not noticing anything missing.
As I recall there was only one release of the uncut Menagerie, on DVD, and that was shortly after it first aired on TV/Cable or whatever. It was a separate stand-alone DVD with two versions of the episode on it as well as other bonus material and cast interviews. I never bought it.