From my point of view it is obvious: The only thing that changed seems to be MojoX::Session (and maybe a few other modules updated with it? Did you also check differences in Mojo::Base or Mojo::Transaction?), so there must lie the fault (at least it would in a perfect world following logical rules ;-).

You might check if the update changed some file permission on files used by the web server or mojo. You might try to debug the mojo modules themselves. Sorry, I don't have anything more than general platitudes advice