Carl's paper said "most QTL effects may be much smaller than expected - not just 1% effect sizes but perhaps effects as small as .1%".

That is fine and surely perfectly expected. Most genes have little or nothing to do with intelligence - and so can be expected to have small effects on it.

The paper didn't say there were no larger effects caused by genetic variation. Genes associated with Fragile X syndrome, Tay-Sachs disease, Neurofibromatosis, etc are known to have larger effects.