It is is working fine here with the layout macro defined inside the loop:
using Plots, Measures
x = 1:10; y = 1:10
const ax = fill(plot(),3,1)
for i = 1:2
l = @layout [a{0.01h}; grid(2,1)]
ax[1] = plot(title="Big Title",
framestyle=nothing,showaxis=false,xticks=false,yticks=false,margin=0mm)
ax[2] = plot(x, y)
ax[3] = plot(y, x)
plot(ax..., layout=l)
savefig("test_$i.png")
end