Hi Rupert,
In the Wright-Fisher model with selection, the expected absolute change in allele frequency shouldn't actually be exactly the same for positive and negative s. Even in the haploid model, we have E[Delta_x] = sx(1-x)/(1-sx). Thus, for a biallelic locus with alleles A and B, when A has selection coefficient s over allele B, this is not exactly equivalent to B having selection coefficient -s over A. I know this might feel a bit unsatisfying, but it's what it is in the WF model, and I think it explains your observation unless I misunderstood something.
Best,