Your file association for .xml files might not be completely set. I'm not sure which one myseq uses, but it could either be the Open funcion or the Edit function. Open is set via the right click -> open with command in explorer. Edit may or may not be set. You can check by using ShellMenuView.
http://www.nirsoft.net/utils/shell_menu_view.html
To make things easy, I'd suggest installing something like Editpad or Notepad+ and just letting it set file associations correctly.