This article, A calorie isn't a calorie claims:
Starch becomes more resistant to digestion when it is allowed to cool and sit after being cooked, because it crystallizes into structures that digestive enzymes cannot easily break down. So stale foods like day-old cooked spaghetti, or cold toast, will give you fewer calories than the same foods eaten piping hot, even though technically they contain the same amount of stored energy.
Unfortunately, the papers they cite seem to be behind paywalls, but is there really that significant of a difference just from bread going stale? Or is this more like the assertion that drinking cold water increases metabolic rates, but the values are so significant as to be lost in the noise?