Short explanation: to reduce wasted bandwidth and make the game fair, and it's a bug that affects probably 2% or fewer maps, so it shouldn't be such a big deal.
Long explanation:
The "crate jump" is caused by roundoff error. Positions are converted from 32bit floats to 16bit short integers when sent over the network. In this conversion, values are rounded toward 0, so if you're at 10.999, it would round to 10, which is lower, but if you're at -10.999, it would round to -10, which is higher. The more values that are sent, the more roundoff error there is. If you're positioned above 0, this means you don't jump as high. If you're below 0, you jump higher. This happens in sandtrap and a couple other maps.
As computers have gotten faster and framerates have jumped up to insane levels, Quake2's poor design of one packet per frame has really shown itself. If you were getting 300fps, that meant you were sending 300 packets every second. I'm sorry, but that's just ridiculous. So I fixed it. In doing so, I reduced the roundoff error, and on a very select few maps, the jump height as well (though it actually increased the jump height on the majority of the maps). Naturally, people complained.
I tried to find a workaround to pacify the babies, and thought I had done so with build 9. See, along with each command the quake2 client sends to the server, it sends backups of the previous 3 commands as well. That way, if a packet or two is lost, the backups are used and it carries on as if nothing happened. Build 9 "cheated" by faking dropped packets. The packets were sent at a set rate, and if your framerate was higher than the packet rate, the extra frames would be put in as "backups" of "dropped" packets. This worked OK in the right conditions, but if packets really dropped, all hell broke lose, because there wouldn't be any backups of those packets, so you'd lag freeze and/or jerk all over the place like a Chihuahua on a rubber leash. Also, if your framerate exceeded the number of commands that could be "backed up." You'd get the phone jack and not be able to move even on your own local server!
