How to debug wrong marginnote alignment

Question

I know this is a long shot since I cannot really post a minimal working example, but I'll try to describe the issue to the best of my capabilities. I'm running pdflatex twice for the compilation.

I have the following testing macro, which produces the expected result at the beginning of the chapter.

\def\myTest{
Text1. \marginnote[left]{right}

Some more text. \marginnote[left]{right}

More text, longer sentence. \marginnote[left]{right}}

Unfortunately, after a few pages, marginnote gets confused.

It looks like the first call to \marginnote[left]{right} fixes the alignment for the following two instances.

One could simply use marginpar. I noticed this issue when trying to use sidecaption, which was putting the text over the figure rather than in the margin.

Original issue

\begin{figure}[H]
  \centering
  \sidecaption{Something.}
  \sidecaption{Something.}
  \caption{Disappeared.}
  \input{inference-figs/activation}
\end{figure}

Answer 1

So, it turns out that marginnote relies on updated aux files. If you have outdated ones, caused by using the \includeonly{} and several \include{} commands, you may incur in some glitches.

The solution was generating the whole document without \includeonly{}.

I decided not to delete this question for indexing purposes. Hopefully, it'll help others not waste plenty of time on bug hunting.

Answer 2

For a systematic approach to identify the trouble makers you may want to adapt this one: How to declutter your main.tex .

Including the preamble an adaptation which converges quickly is „50:50“. If your relevant document part consist of A+B, create two versions, with A or B alone. Say A compiles, but B generates errors. Next dive into part B and repeat.

Many times this ends up at faulty or „shady“ lines of code. Sometimes the (nothing-to-see-here) result forces you to think outside the box, which might suggest deleting a file as you did.