It's possible the site is overloaded to the extent that ajax messages are getting lost (I have no resend mechanism right now).
Out of interest though, what browser/os are you using?
I tested a little more, and the worst problem seem to be that in a situation like this:
EDIT: I can't get the formatting to work, but picture a horizontal "HELLO" with "LEMON" coming off the HELLO's second "L".
... and you click on the "l" in lemon, it highlights "hello". You really should NEVER have ambiguity like that. Maybe a second click should alternate between them.
That's exactly what it does, for me. Thanks, I'll test with ff1.5 and see if I can reproduce this.
But lesson learned: Other people are going to be stupid, too.
And apparently my earlier problems were due to latency. If you go too fast, the updates come up a little oddly, and the letters switch 1) When you type, 2) A moment later to something historical, and 3) Back to what you typed.
The puzzle itself looks nice, but I think there is a slight contrast problem with the black-to-white fading of the white squares against the black background. It just feels slightly off, no big deal.
However: You've clearly got some bad bugs in this. I went to answer "Country whose capital is Tehran" and it took a good minute before I could enter the answer. I clicked on it, the correct row highlighted green, and when I went to type "I", the second letter filled in "I". Then I pressed the first square of four, but the attached (horizontal) row highlighted. So I clicked on the IRAN squares again, typed I-R-A-N, it didn't work, and after some fiddling, I typed it again, and it seemed to enter I-I-A-N, then I-I-I-N, then it highlighted the last square, which flashed I then R then A then N as I typed them, then finally I typed it again, it seemed to go I-I-I-I, then changed to IRAN, finally. ???