MCT oil is not a natural oil. It is reconstructed by an industrial process. As a result, it has different properties that could produce your observed effects. First, it is extremely thin in viscosity compared to natural fats and could easily "wick" down a hair strand from the folicle. Second, the body might not partition it identically to natural fats, and more might be excreted in hair folicles than average, and less might be stored in fat cells than average. Third, the low viscosity might make it better at dissolving molecules with scent, or in releasing scented molecules that might otherwise remain embedded within the hair matrix. And lastly, maybe your olfactory sensitivity goes up a notch when you use MCT.
Switching to coconut oil might give you a comparison. Using other people's noses might give you a point of comparison. Do they think that the smell of MCT oil and your hair are the same or similar? Is there a time course for the smell to increase after you shampoo your hair? Is the smell stronger at the hair roots than at the hair ends? If you work out or sun bathe, is the smell stronger?
Some hair-care products cause chemicals to soak into the hair matrix, which might later come out differentially. As an illustration, consider a plastic salsa bottle. When freshly rinsed, you can smell the chili-pepper scent. But as the bottle ages, and is washed repeatedly, the scent dissipates. One bicycle rider used a salsa bottle to replace his stolen water bottle. It did not take long for the slight smell of chili peppers to dissipate, but months later, when he switched from filtered water to alkaline-reduced (electrolyzed) water, the taste of the chili-pepper increased a hundredfold (stronger than ever). Alkaline-reduced water has smaller cluster size and makes a better solvent to facilitate the pepper-scent chemicals from diffusing out of the plastic. Mct oil is a better solvent than regular fats. Perhaps you had your hair dyed, straightened, bleached or strengthened some time ago and if you think about the smell then, it will remind you in some way to the scent now.
Good luck figuring it out. ---Steve