We report a novel soft x-ray nanodiffraction study of antiferromagnetic domains in the strongly correlated bylayer manganite La$_{0.96}$Sr$_{2.04}$Mn$_{2}$O$_{7}$. We find that the antiferromagnetic domains are quenched, forming a unique domain pattern with each domain having an intrinsic memory of its spin direction, and with associated domain walls running along crystallographic directions. This can be explained by the presence of crystallographic or magnetic imperfections locked in during the crystal growth process which pin the antiferromagnetic domains. The antiferromagnetic domain pattern shows two distinct types of domain. We observe, in one type only, a periodic ripple in the manganese spin direction with a period of approximately 4 micrometer. We propose that the loss of inversion symmetry within a bilayer is responsible for this ripple structure through a Dzyaloshinskii-Moriya-type interaction.