- The genes for schizophrenia are still the powerful causal agents we thought we'd discover, but they aren't common - a different mutation accounts for the phenotype in most cases, allowing such mutations to slip through the net of population-based studies.
- The set of genes for schizophrenia, while still collectively powerful, is composed of a plethora of genes, each with a tiny additive effect on the likelihood of developing schizophrenia.
- Schizophrenia is not one disease, but several, each of which has its own powerfully causative set of genes.
- Schizophrenia isn't as genetic as psychiatrists think. Genes only play a small role.
The only option that isn't persuasive is the last one, as it is actually reasonably easy to provide an estimate of schizophrenia's heritability. (Compare identical twins reared apart to identical twins separated at birth. Any variation in schizophrenia incidence must be due to environmental differences.) Such studies indicate that schizophrenia is reasonably highly heritable.
Of course, this only deepens the paradox. If schizophrenia is so heritable, where are the genes? There are actually other options to add to the above list. If you're interested in the 'big picture' problem exemplified by the case of schizophrenia, try this accessible article from the Evolution and Medicine Review, entitled (helpfully enough), "Why are there so few genes of major effect on highly heritable disorders?"