Menukeys needs to be loaded after BibLaTeX.

example/mu/example.dtx

@@ -419,7 +419,6 @@
 \usepackage{amsthm}
 \usepackage{amsfonts}
 \usepackage{url}
-\usepackage{menukeys}
 \begin{document}
 %<*econ>
 \makeatletter
@@ -788,8 +787,8 @@ the bibliography section will appear in the table of contents.
 The \texttt{biber} command needs to be executed from within the
 directory, where the \LaTeX\ source file is located. In Windows,
 the command line can be opened in a directory by holding down the
-\keys{Shift} key and by clicking the right mouse button while
-hovering the cursor over a directory.  Select the \menu{Open
+\textsf{Shift} key and by clicking the right mouse button while
+hovering the cursor over a directory.  Select the \textsf{Open
 Command Window Here} option in the context menu that opens shortly
 afterwards.
 
@@ -835,8 +834,8 @@ corresponds to the main locale of your thesis -- such as
 The \texttt{texindy} command needs to be executed from within the
 directory, where the \LaTeX\ source file is located. In Windows,
 the command line can be opened in a directory by holding down the
-\keys{Shift} key and by clicking the right mouse button while
-hovering the cursor over a directory. Select the \menu{Open Command
+\textsf{Shift} key and by clicking the right mouse button while
+hovering the cursor over a directory. Select the \textsf{Open Command
 Window Here} option in the context menu that opens shortly
 afterwards.
 

guide/mu/guide.dtx

@@ -14,7 +14,6 @@
   sortlocale=auto
 ]{biblatex}
 \addbibresource{guide.bib}
-\usepackage[os=win]{menukeys}
 \makeatletter
 \thesissetup{
   title=A fithesis3 user guide for the \thesis@english@facultyName,
@@ -51,6 +50,8 @@
   capabilities, this document was typeset using the
   \textsf{fithesis3} class.}
 \makeatother
+\thesisload% The menukeys package does not play nice, when it is
+  \usepackage[os=win]{menukeys}% loaded before BibLaTeX.
 \begin{document}
   \makeatletter\thesis@preamble\makeatother
   \chapter{Introduction}