LaTeX.org

It is in the ncctools bundle,
http://www.ctan.org/tex-archive/macros/ ... /ncctools/

I gave up and just set all my equations to fleqn in the preamble.

I was wondering if you had figured out the problem yet.

It works fine if you change \SetKwData{H}{h} to \SetKwData{HH}{h}, however I have no idea why it thinks H is protected variable..?

p.s. you probably already know, but as for the other {,$ errors, you are missing two $$ around a \leftarrow ...

1) The <algorithms> package is also very nice if you have to write a lot of pseudo-code.
http://www.ctan.org/tex-archive/macros/latex/contrib/algorithms/

For example, try running this to get a version of your pseudo-code from above:
\usepackage{algorithm,algorithmic}
\usepackage{amsmath}

\begin ...

I am looking for a way to have two different equation alignments in the same document, in this case a rather long thesis.

For the main body of the thesis, I would like (and currently have) the default alignment of equations-centered and eqno-right. For the appendices however, as they are almost ...