I have found that many fish are pretty fearless as very young fish, and get more wary of humans as they age. Some grow out of this at full size. As juveniles and adults, I would assume their instincts are sharper about avoiding potential predators.
The environment is very important for avoiding skittish fish. What does your setup look like? Lots of cover (especially in top 50% of tank) or mostly open? How bright is your light? The cuban is completely alone, or any dithers?
In general, I find American cichlids seem to be more comfortable and less skittish in more dimly lit tanks, with adequate cover in the tank. Real or fake plants, manzanita wood etc can be used. Solo fish can often become shy as well, and keeping in communities/shoals or with dither fish can help- but you need a large enough tank attempt either, and I wouldn't try this with a cuban in less than a 100 gallon tank. A 45 gallon is quite large for a 2" fish, and somewhat small for a 5" fish, he may also just be outgrowing the tank and feeling cramped.
Alternatively, he could have parasites or an illness like you suspect. I would look for other signs like white stringy poops or anything visible on the fish .