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If you mean the suggestion about converting it to CSV files for pgfplots, I admit that I wasn't sure how to respond to that. Unless I misunderstood what you're saying (which is always possible :) that sounds like it would simply bypass the problem, which is specific to tikz. But please feel free to ...

Unfortunately, it seems this problem is one where making a self-contained minimal example is not possible and also takes much more than just half an hour (I've just spent over 3 hours on it and now the .tex file is too big to attach). It is very elusive and I have encountered several red herrings ...

Update: I have discovered that the small, squashed up image is due to not resetting the figure dimensions just before calling, however this still does not resolve the problem of some images just not forming at all.

When I isolate each tikz input into its own .tex file and include only this file ...

Fair enough - I just wasn't sure which code bits to display and was hoping someone would recognise it as a similar problem.

In my main project .tex file, I have:
%% Packages for Graphics & Figures %%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{graphicx} %%For loading graphic files
\usepackage{caption ...

I apologise for the long essay, but it's an obscure error with no useful messages.

I'm writing up my thesis and want to include a lot of MATLAB plots. I'm using matlab2tikz to export the plots into tikz files and, for those which work, they look fabulous in the LaTeX result, so I'd really like to ...