Unlike the View->Processes... menu item that remember which processes has been deselected, the View->Variables... does not. Example: You are simulating a system with lots of variables. You decide to deselect half of them. If afterwards want to deselect a single extra variable, you have to again deselect all the variables you deselected the first time.
I have checked in a fix. While I was at it, I also replaced the old dialog for choosing visible variables/processes. The new dialog uses a list of check boxes in a scroll pane rather than the two column view used in the old dialog. The dialog is works better for systems with a large number of variables/processes.