Are you eating any processed foods, Mr. McInnes? Like the protein supplements? Do they contain any form of sugar? I don't mean just sucrose, also fructose, anything that converts to sugar in the body. Please do consider watching "That Sugar Film." You may be surprised by what you see - 1,000 calories is a very low budget, and within it, I can understand how you would need to use a supplement to get adequate nutrition.
"Calories" aren't equal and it isn't about thermodynamics exclusively - the body metabolizes different foods differently and "calories" are measured in a brute force way (burning, right) that isn't the same as how the body digests food. For example, whole fruits metabolize differently than juice, which is why a parent should give their child a whole orange, not a glass of orange juice. Blessings and white light for your health and well being.