As was noted before, the boot loader for Linux was seen on the screen prior to the Windows desktop coming up. Why? Hard to say for sure, but I would guess that each of the machines actually has 2 or 3 "instances". Meaning, the computer could be booted with the "production" Windows XP instance (not Vista since it requires too much to run), a testing or develop instance, and possibly another one for additional testing and development. My guess would be one (or more) are Linux.
I found that interesting.
Now, why would Disney choose Windows? Keep in mind, this is just for a display being shown to you. It's not like it is controlling the ride or anything important. My guess is that Disney has a fairly large Unix computer controlling the ride. So why choose Windows? Two reasons. First, it's fairly inexpensive and is capable of doing the job. Second, there are a plethora of programmers around for it. If it were me, they would have chosen Linux, or another embedded version of Unix. But people capable of getting the job done are harder to find, and more expensive to hire. Chances are they contracted the programming out, kind of like they did for Test Track. Remember how Test Track opened 18 months behind schedule? That was due to crappy software from the contractor they hired. The TT fiasco was a very interesting story.
Most likely the animation in SSE was from MacroMedia Flash, but who knows for sure. I would bet that the instance that runs the actual animations you see is locked down enough that throwing anything away is one step short of impossible. The right thing to have done was when the Grub screen came up, see if you can escape to the (possibly hidden) menu for boot options. Then see if you can boot to another instance.
I graduated with degrees in Electrical Engineering and also Computer Science & Engineering. When I was in college they taught us computer assembly language, C, and other more "hard core" languages capable of doing real brute force tasks. But unfortunately, as the computer market changed, and now 80% of the jobs out there are for Windows, the schools teach what the market(s) want. So many people in engineering schools are being taught to use Micro$oft tools for development. This way the people who graduate can find a job readily. But so now Disney has a harder time finding people capable of doing things "old school".
I guess it boils down to, how much money does Disney have to do the job at hand. They have a budget. They must stay within that budget. If they did things a "different" way from how they did, that would mean less entertainment value for all of us to see/enjoy.
By the way, people complain about Windows a lot. Some of the complaints are legit, while others are not. If you lock down a Windows machine sufficiently, it can be a pretty stable and secure machine. The real problem is all of the wizards, and defaults Micro$oft added. Most machines have all of the default settings left on, and "Uncle Bill" ships their machines with most things turned on so users don't have to know a thing about their machines in order to fully use them. This of course is a huge mistake. User should have to read a manual for a few hours before using their computers, even though this would mean less people buying computers.
(oops, got off track there)
OK, so now I am going to get some flames Didn't start out that way.