I spent a long time suspecting that these repeats were 'correia' elements, a very short but complex transposable element common in Neisseria genomes. But I couldn't find a clear illustration of the correia consensus, and I couldn't find a good match between the correia sequences I could find and the sequences of the stray motif in my DUS dataset.
Finally I realized that I could try using the Gibbs motif sampler to characterize the motif. So I took my set of intergenic sequences, used Word to delete all the perfect DUS (both orientations), and asked Gibbs to find a long motif. I didn't know how long the stray motif actually was, so I tried guessing 20 bp, then 30, then 40. But this didn't seem to be working - instead of finding a couple of hundred long correia-like motifs it would find a couple of thousand occurrences of something with what looked like a very poor consensus. So I seeded the sequence set with about 20 occurrences of the motif taken from the dataset where I'd first noticed it.
Gibbs again returned about 1500 of what looked like poor-consensus occurrences, but this time I had a bit more confidence that this might be what I was looking for, so I trimmed away all the notation and posted them into WebLogo. This gave me a palindromic repeat that I'll paste below later, and a bit of Google Scholar searching showed me that this isn't correia at all, but a short repeat called RS3, known to be especially common in intergenic sequences of the N. meningitidis strain I'm using.
So now I can write a sensible manuscript sentence explaining what these repeats are and why I'm justified in removing them from the dataset.