I've managed to make it work again.
First if you´ve used edgecolor and facecolor, this isn´t working.
I used XColor and YColor now.
then I´ve put my new waitbar into handles:
h = waitbar(0,'  ','Visible','off' ); %   
    % Close the default figure 
      % The child of the waitbar is an axes object.  Grab the axes 
      % object 'c' and set its parent to be your figure f so that it now 
      % resides on figure f rather than on the old default figure. 
      c = get(h,'Children'); 
      set(c,'Parent',handles.thisfig);  % Set the position of the WAITBAR on your figure 
      set(c,'Units','pixels','Position',[1 2 0 18]);  
      set(c,'XColor',[1,0.8,0.4]);
      set(c,'YColor',[1,0.8,0.4]);
       set(c,'Color', [0.09,0.09,0.09]);
      c.Visible = 'On';
      handles.splash_waitbar = c;
      handles.splash_waitbar.Visible = 'On';
in my other File, I use the "Position value" to increase the bar as I want to. while you have to multiply your "waitbar"-expression with the max-width of the bar.
           value = 798 *((step) / (maxstep));
              set(handles.splash_waitbar,'Position',[1 2 value 18]);