As I had theorized in an earlier post, I suspected that the tower I had designed was staying together because of the use of cables holding the tower together. I was wrong.
Subsequent testing has shown that the reason my tower doesn't blowup is because of the "short" diagonal joists. The long ones break. This seems to be in direct contradiction with previous observations.
Additionally, I have been able to increase the number of joints on a story without causing it to blow up, but I have to use short diagonals to do it. Longer diagonals cause stress failure.
Perhaps this is why the small joint boxes don't automatically explode. If they did, it wouldn't make for much of a game. 
I'm working on a new tower level right now, to see what other factors are at play, but I have sucessfully built a single column in the entire vertical space without causing any broken links. That is 640m high. It is also the most computationally complex level I've seen yet. My computer is uncharacteristically slow when testing. I'll make it available when I'm done.
Update: At about ũ.6 million, I ran into the same problem as someone else about their bridge disappearing. I hit the links limit, and consequently wasn't able to build beyond the 5th story. I will try and cut back on some building materials and the design. I know you all are counting on me, but it is late, and I'm going to give up for the evening.
Good luck to everyone who submitted a bridge for the contest, the results come out in T-7:48:23.624...
(Edited by baggio at 5:14 am on Oct. 29, 2001)