That sounds pretty much it Pete. I'm not saying that's what happened for certain, but it does sound feasible.
Any droplets of the fuel/food source that become airborne, through any number of ways, will eventually settle somewhere. In the humid atmosphere of a cave, it won't be long before that fuel will become , for want of a better phrase, coated in water, and to some extent, and using Avtur as a Gide, mixing with it. At this point, the fungus spores will start to grow in the area where the two meet, the Water/Fuel Interface, as it's known.
I've had a look at the treatment procedure, and (in Aircraft, so it's only a guide here), it has to be first "Physically Removed" , in this case, probably scrubbed off with a brush, and then treated with a fungicide to kill it. What sort would be appropriate in a cave, I wouldn't like to guess.
The problem with this is that the Fuel/Food Source in My Aeroplane, and Alex's Boat, is drained out first, here that does not seem to be an option. So until the initial contamination is gone, it'll probably be a loosing battle to remove it.
Lastly, in this situation, it might just actually help to get rid of the problem, by eating it, but it won't be a quick job, several years at least.