Different values for data being stored and used by the code for same variable

vref = xg(1:model.nReactions);

% x -> alpha(tk,EnzInd)
a_ = xg(model.nReactions+1:model.nReactions+model.nEnz*length(t));
for tk = 1:length(t)
    a(tk,:) = a_(model.nEnz*(tk-1)+1:model.nEnz*tk);
end

% Alpha to reaction matrix i_th reaction times j_th alpha
a_mat = zeros(model.nEnz,model.nReactions);
for j = 1:model.nEnz
    if j == model.nEnz
        a_mat(j,model.EnzInd(j):end) = 1;
    else
        a_mat(j,model.EnzInd(j):model.EnzInd(j+1)-1) = 1;
    end
end

A= []
% v_i(i,tk) = v_ref_i * a(j,tk) * b(tk)
for tk = 1:length(t)
    aa = a(tk,:)*a_mat;
    for ii = 1:model.nReactions
        vi(ii,tk) = vref(ii)*aa(ii)*b(tk,ii);
        A = [A; vref(ii) a(ii) b(tk,ii) vi(ii,tk)]    %%values of vref displayed here are different than those stored in resultsCC1.vref
    end
end


% v_e(i,tk) = v_i(j1,tk)*S(i,j1) + v_i(j2,tk)*S(i,j2) +...
ve = zeros(model.nMetabolites,length(t));
for tk = 1:length(t)
    for ii = 1:model.nMetabolites 
        for jj = 1:model.nReactions
            ve(ii,tk) = ve(ii,tk) + model.S(ii,jj)*vi(jj,tk);
        end
    end
end

%Normalize a
a = a./repmat(a(1,:),size(a,1),1);

%% Save Results in a structure
resultsCC1.a       = a;
resultsCC1.vref    = vref;
resultsCC1.b       = b;
resultsCC1.vi      = vi';
resultsCC1.ve      = ve';
resultsCC1.ssr     = fg;

[per isakson]

You need to be more specific!

See TUTORIAL: how to ask a question (on Answers) and get a fast answer