blastn short anomaly, query and reference working in combination with other querys and references

Question

I'm trying to blast (task blastn-short) an 11bp sequence against a genome (GCF_000715135.1_Ntab-TN90_genomic.fna) and get no results, despite the sequence being present (confirmed with grep). The query file and script works when blasting against several other genomes that are either masked or unmasked. Adding four bases that are found in the genome to the query file returns results. I'm using command-line blast+ 2.15.0 but get the same results with 2.13.0. Given the above I wouldn't think the following would matter but tried anyway with no luck. Re-indexing the genome in question. All combinations of upper/lower-case and header/no header description. Has anyone run into anything like this before?