Hi Neil: Is the fragment you are using for probe subcloned into
bluescript or a related vector? Sometimes when gel purifying your
insert DNA from the vector it's cloned into you can get minor vector
contamination with your insert. This can happen if you run the gel
too quickly. I've also been told that degraded vector fragments can
co-purify with your insert. Although the contamination will be
minor, when hybing against large amounts of plasmid DNA you'll get
a signal. I don't know if this explains your situation, but I hope it helps.