Please follow this procedure from our Wiki: http://wiki.processmaker.com/index.php/ ... and_higher
in order to upgrade from any version of ProcessMaker prior to 2.0.
For Windows users, please do as the Wiki says and use the .tar.gz source file in order to upgrade any version you may have running to version 2.0. The Windows installer .exe file is only for doing clean installations and won't upgrade an existing version of ProcessMaker, in fact it may even damage it.
And please remember to always backup your workspace, application and database before performing an upgrade from any version to any other version.