Sorry about your upgrade probem. Unfortunately that is fairly typical of installs done by these third party installers. They just do not get it right.
Maybe someone on the forum uses Bluehost and can tell you how to install without SimpleScripts. Otherwise you will probably have a bit of a wait. 1.4.0.1 was released end of January. 1.4.4, the current bug fix version of the 1.4 cycle, Was released early May--5 months have passed and you have no bug fixes!