Because, giant newb faggotry

I'm working on a little project to learn Python, but I can't seem to get past the baby steps. Some iterations of my loop are behaving a little erratically, not catching certain letters and shifting them.

http://pastebin.com/YDR1mQhE

Not looking for code for an answer, but maybe some information that will put me in the right direction.

>>1
Also, can you please stop writing str.replace(x, y, z) instead of x.replace(y, z)?