Update July 4.  
I ran an identical dummy app on both the Small Form Factor (SFF) machine and the Precision Tower (PT).  The dummy app is the same one I displayed above, it had two axes and 8 buttons arrayed around the UIFigure.  The only change I made from the version displayed above was to put in a startup function that output the positions of all the components into a .mat file.  Just for completeness, I will post the dummy app text at the end of this description.  I wrote the postions into an excel file for display.  Here is the result of running in on the two machines.
Positions and display on execution on the Precision Tower (the display matches the appearance in app designer)


Postions and display after app execution on the SFF machine (the display does not match the appearance in the app designer):


The positions of all of the app components and the UIFigure are identical in both cases, but on the SFF the display is distorted.  I would very much appreciate any idea why this could be happening and what I can do to fix it.  As it is, this rather generic pc is useless for MATAB apps.
Here is the text of the dummy app for reference, apologizing for the space taken but I want to be absolutley clear.  
classdef app1 < matlab.apps.AppBase
    % Properties that correspond to app components
    properties (Access = public)
        UIFigure  matlab.ui.Figure
        Button8   matlab.ui.control.Button
        Button7   matlab.ui.control.Button
        Button6   matlab.ui.control.Button
        Button5   matlab.ui.control.Button
        Button4   matlab.ui.control.Button
        Button3   matlab.ui.control.Button
        Button2   matlab.ui.control.Button
        Button    matlab.ui.control.Button
        UIAxes2   matlab.ui.control.UIAxes
        UIAxes    matlab.ui.control.UIAxes
    end
    % Callbacks that handle component events
    methods (Access = private)
        % Code that executes after component creation
        function StartUp(app)
           uipos = app.UIFigure.Position ;
           axespos = app.UIAxes.Position;
           axespos2 =  app.UIAxes2.Position;
           butpos = app.Button.Position;
           butpos2 = app.Button2.Position;
           butpos3 = app.Button3.Position;
           butpos4 = app.Button4.Position;
           butpos5 = app.Button5.Position;
           butpos6 = app.Button6.Position;
            butpos7 = app.Button7.Position;
            butpos8 = app.Button8.Position;
            save("app1.mat","butpos8","butpos7","butpos6","butpos5","butpos4","butpos3","butpos2",...
                "butpos","uipos","axespos","axespos2");
        end
    end
    % Component initialization
    methods (Access = private)
        % Create UIFigure and components
        function createComponents(app)
            % Create UIFigure and hide until all components are created
            app.UIFigure = uifigure('Visible', 'off');
            app.UIFigure.Position = [100 100 640 480];
            app.UIFigure.Name = 'MATLAB App';
            % Create UIAxes
            app.UIAxes = uiaxes(app.UIFigure);
            title(app.UIAxes, 'Title')
            xlabel(app.UIAxes, 'X')
            ylabel(app.UIAxes, 'Y')
            zlabel(app.UIAxes, 'Z')
            app.UIAxes.Position = [116 211 300 185];
            % Create UIAxes2
            app.UIAxes2 = uiaxes(app.UIFigure);
            title(app.UIAxes2, 'Title')
            xlabel(app.UIAxes2, 'X')
            ylabel(app.UIAxes2, 'Y')
            zlabel(app.UIAxes2, 'Z')
            app.UIAxes2.Position = [116 14 300 185];
            % Create Button
            app.Button = uibutton(app.UIFigure, 'push');
            app.Button.Position = [433 31 100 22];
            % Create Button2
            app.Button2 = uibutton(app.UIFigure, 'push');
            app.Button2.Position = [30 31 100 22];
            app.Button2.Text = 'Button2';
            % Create Button3
            app.Button3 = uibutton(app.UIFigure, 'push');
            app.Button3.Position = [17 161 100 22];
            app.Button3.Text = 'Button3';
            % Create Button4
            app.Button4 = uibutton(app.UIFigure, 'push');
            app.Button4.Position = [17 293 100 22];
            app.Button4.Text = 'Button4';
            % Create Button5
            app.Button5 = uibutton(app.UIFigure, 'push');
            app.Button5.Position = [17 416 100 22];
            app.Button5.Text = 'Button5';
            % Create Button6
            app.Button6 = uibutton(app.UIFigure, 'push');
            app.Button6.Position = [433 141 100 22];
            app.Button6.Text = 'Button6';
            % Create Button7
            app.Button7 = uibutton(app.UIFigure, 'push');
            app.Button7.Position = [433 273 100 22];
            app.Button7.Text = 'Button7';
            % Create Button8
            app.Button8 = uibutton(app.UIFigure, 'push');
            app.Button8.Position = [415 416 100 22];
            app.Button8.Text = 'Button8';
            % Show the figure after all components are created
            app.UIFigure.Visible = 'on';
        end
    end
    % App creation and deletion
    methods (Access = public)
        % Construct app
        function app = app1
            % Create UIFigure and components
            createComponents(app)
            % Register the app with App Designer
            registerApp(app, app.UIFigure)
            % Execute the startup function
            runStartupFcn(app, @StartUp)
            if nargout == 0
                clear app
            end
        end
        % Code that executes before app deletion
        function delete(app)
            % Delete UIFigure when app is deleted
            delete(app.UIFigure)
        end
    end
end






