How can I change the default open directory in PHPED? I do not want my files / workspaces to be in the default path the PHPED wants. So everytime I go to create a new project it default to [user dir]\application data\phped . My files are not in this path.

Sorry, I'm not sure what you mean. There is no such thing as "default open directory" in PhpED. If you run PhpED for the very first time, yes, it offers one in %APPDATA%\NuSphere\PhpED\Projects. Don't you agree that it has to offer a particular directory? If you select another, it will remember you choise and offer that next time. No problems so far.
Regarding files in the projects, everything depends on the project root directory, it's because the project file should be saved in one of the directories in the project tree. Finally you can right click on directory of your choise and select New File in the popup.

Anyway, if you experienced a problem, please contact support.