Hello
I propose to use the ActiveX automation server. From Matlab is is very easy to call executable vi and make it do what you want. It is stable, fast and easy.
useful commands are (just coppied from my code - hope you can follow):
If you test it through the development environment you use:
LVapp = actxserver('Labview.Application');
if it is executable you use:
LVapp = actxserver('Your_App.Application');
%call your vi in to memory
viPath = 'Your_top_vi.vi';
vi = LVapp.GetVIReference(viPath) ; % 'Load the vi into memory
% 0 - invisible, 1 - visible
%vi.FPWinOpen = 0;
vi.FPWinOpen = 1;
%if you want to set control values you use:
invoke(vi,'SetControlValue','Your_Control_Label','Your_value');
% if you want to execute the vi you use:
vi.Run;
Hope it helps
Pawel