I am not a military pilot- my only experience of military flying was in the UAS. However, I have spent the last five years flying a largely electronically-controlled aircraft. Glitches that appear, then mysteriously disappear and leave no trace, are a weekly occurrence within our fleet- with earlier versions of the software, they were a weekly ocurrence for most individual pilots. These glitches range from spurious warnings in the EICAS, to lift dump spoilers that did not open on a landing on a short wet runway. (They did, however, open during flight the following sector. No trace was evident in the inbuilt maintainance computer afterward).
In this case it seems likely that the flight was operating relatively smoothly until shortly before the Chinook approached the Mull. Any temporary malfuntion need not have been of the magnitude of Thud's example- even a spurious warning at the wrong time can be a serious distraction. Indeed, warnings suspected to be spurious can be more distracting than genuine warnings.
JP, if we accept your theory that the crew misidentified the fog alarm as the lighthouse, is this level of distraction (perhaps allied with the crew believing they needed to get the aircraft on the ground immediately) a possible explanation?