The key to solving this is to realise that a "regular" compilation process sends your document through pdfLaTeX in PDF mode, and in order to do the psfrag replacements the graphic is sent through pdfLaTeX in DVI mode.

Therefore, conditional commands for either the main document only or each graphic only can simply use \ifpdf:

\ifpdf
  % setup for the main document only
\else
  % setup for pstool images only
\fi


And so in your case:

\ifpdf\else
  \setbeamertemplate{navigation symbols}{}
\fi


This is entirely unmentioned in the documentation, so I'll go fix that up now.

Using pstool with beamer
From the perspective of a Ph.D. student, how much of an added value is it to have your own presentation slides layout, that is used consistently throughout your Ph.D. conference presentations and other talks (and possibly throughout your academic career afterwards)?

Here is one such example from the Computer Science community.

This as as opposed to using existing Beamer templates with LaTeX, or built-in PowerPoint templates, or simply preparing each presentation on its own (without a specific layout).

A couple of axes I can think along:


Creating a signature layout that distinguishes one in their community
Ease of preparation of presentations (especially over time), maybe overcoming constraints with existing templates.


Note that I am not concerned with the question of content, but just design and layout.
