For one of my repositories, it doesn't remember the name of the repository I am pulling and pushing to. I don't have this problem with any of the other repositories on my machine. Is their any way to fix this?
As of version 3.0 there is no "setting" for choosing the default URL. Instead you must create an alias of "default" for the URL that you want.
To do so, from workbench, right click on the repository and select settings. Click Edit File and add a line (see below) that specifies the default path to the desired repository.
default = URL of repository