You should use flipud() or flip(_,1) or just use indexing (and do vertical concatenation with ; rather than horizontal concatenation with ,):
% some data similar to yours for the purpose of filling between:
f2 = linspace(0,30,64*30+1).';
yconf = -40*sin(f2)-40+[0 -20];
plot(f2,yconf);
xlim([5 30]);
% fill using flip():
figure()
x2 = [f2(321:1921,:); flip(f2(321:1921,:),1)];
inBetween = [yconf(321:1921,1); flip(yconf(321:1921,2),1)];
fill(x2, inBetween, 'g');
xlim([5 30]);
% fill using indexing:
figure()
x2 = f2([321:1921 1921:-1:321],:);
inBetween = [yconf(321:1921,1); yconf(1921:-1:321,2)];
fill(x2, inBetween, 'g');
xlim([5 30]);
