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That's fantastic. Everything aligns perfectly. I'm actually going to replace \binom with the equivalent version of that command just for the alignment. Thanks so much!

I was looking for ways to extend the \binom command to include more than 2 arguments. The formatting of \pmatrix was not satisfying for me, so I came up with a custom command based on \genfrac from amsmath:

\newcommand\triplet[3]{\left(\genfrac{}{}{0pt}{0}{#1}{\genfrac{}{}{0pt}{0}{#2}{#3}}\right ...

Ah, that does it. Thanks!

The error involves the use of \input , so a complete minimal working example consisting of one file is obviously impossible.

I have combined two of the files, so the desired and the buggy behavior are shown together. The new example is attached (including both the source and compiled PDF so the ...

The working example contains 5 files, while the attachment upload limit is 4. The five files are as follows:
doc1.tex
doc1.pdf
doc2.tex
sec1.tex
doc2.pdf

You can now find these on my webspace:
http://kjplanet.com/input-bug/

I have encountered some strange behavior from \hfill when using \input for a section of my document.

A minimal working example is attached. doc1 shows the desired behavior without the use of \input . doc2 shows the observed behavior when including sec1 using \input : the \hfill on the last line is ...