Hey, this is the first time I've ever done a logic game of this type, I quite like it.
A few suggestions / notes:
At first I instinctively build my machines so that all the inputs for the branches would always go in the side with no arrow, I would suggest making it noted that that isn't needed.
A further increased speed would be really nice, say like a tile or more per frame if possible.
On the androids level a solution of mine would fail because I would write something before removing something, so I have to go with a slightly less elegant solution. Removing one pair on the second really long one would fix that.
Some of the early ones I could more or less brute force solutions that would still solve it, but only with shorter strings, and would horribly fail with longer ones (I would basically need more room the longer the string is.) Going back I was able to redo them with much more elegant solutions that solve it faster and could solve strings of any size. I don't know if you want to allow the more hackish solutions or not, but I thought I'd mention it.
Speaking of long strings to make sure people aren't using non-scalable solutions, please please please make the long strings very last. It's very annoying to wait for it to simulate a long string (which is made even worse that the first working copy is probably inefficient) only for it to fail at an empty test or something silly like that that takes 5 seconds to fix and 3 minuets to wait for it to simulate the long strings again.
Also make the fast forward button apparent, I didn't notice it until I read someone mention it in this thread.
I would suggest making it so linked ones don't over-ride your previous ones at all, nor grant you anything on running them. Sure people could still just copy the design over, but I would use linking more to show of my solutions to people who have beat it in a different way, and less to give other people solutions to advance.
I beat generals before you fixed the text being broken, by playing around with the level to see what would work, is this a valid solution to for all numbers, and not just the ones fed? (I honestly can't figure out how I solved it, I only know it works) :
http://pleasingfungus.com/Manufactoria.swf?lvl=22&code=p12:2f3;c11:3f3;c11:4f3;c11:6f0;i11:5f5;c12:4f3;c12:5f3;c12:6f3;c12:7f3;c12:8f3;c12:9f3;c12:10f3;c12:11f3;c12:12f3;c11:2f3;p10:6f0;c10:7f0;i9:7f6;c8:7f1;c8:6f1;c8:5f1;c8:4f1;c8:3f2;c9:6f3;c9:8f2;c10:8f2;c11:8f2;p9:3f3;c10:3f2;p10:5f1;c9:5f0;c13:2f0;It beats quite literally the longest string I can throw at it, which means you win!
With far more effort than doing it 'properly' would take! (Or far more parts, at least.)
Congrats!
See, that's what I mean by "most people don't program for scalability

(Just joking. And I better don't tell you that you could break my construction quite easily by having for example more reds in a row than I have switches on the red side...)
By the way, I finally got a
correct solution. And yeah, that was way harder than the other (the former androids).
I don't believe that solution would work if either red or blue had a greater amount than the other by two or more. This is how I solved it to work for all possible strings: (Accidentally killed my old optimized version, this is slightly different, thought it may be a tad faster or slower, I really don't know)
http://pleasingfungus.com/?lvl=8&code=c12:2f3;c12:3f3;c12:4f3;c12:5f3;p12:6f3;g11:6f0;g13:6f2;p10:6f0;p14:6f2;r14:5f3;p14:7f3;p10:7f3;r11:7f0;b9:7f2;b13:7f2;r15:7f0;c12:7f3;c12:8f3;c12:9f3;c12:10f3;c12:11f3;c12:12f3;q14:8f3;q10:8f1;c9:8f0;c8:8f1;c8:7f1;c8:6f1;c8:5f1;c8:4f2;c9:4f2;c10:4f2;c11:4f2;c15:8f2;c16:8f1;c16:7f1;c16:6f1;c16:5f1;c16:4f0;c15:4f0;c14:4f0;c13:4f0;b10:5f3;Also, here is my solution before I went make and optimized it (and thought I had to feed things a certain way):
http://img521.imageshack.us/img521/5617/confusedt.pngI have no clue what I'm supposed to do for school teachers, can you explain in further what I'm trying to accomplish.
I have four levels left. I have to figure out Admirals and School teachers, Children just popped up but it doesn't look hard, and I'm looking forward to finding out what the challenge is for the final locked one.