It looks like that the generated HTML files contain erroneous class links which are specific to your machine of generation rather than relative and universal.
Example:
"Modelica media library" on http://kdavies4.github.io/FCSys/ points to file:///C:/Program%20Files%20(x86)/Dymola%202014/Modelica/Library/Modelica%203.2.1/help/Modelica_Media.html#Modelica.Media
Solution:
a. use OpenModelica instead of Dymola to generate the help
b. figure out what to tweak in order to get Dymola to generate the links correctly.