Are you reading off the dash? If so, this question is irrelevant.
There are a number of factors that go into it... Has you trans finished its relearn (and did you actually let it do so, usually takes several hundred miles)? Which tune are you running? Towing and performance tunes both have different shift points/tc lockup strategies. Generally guys find the best mpg tunes are somewhere in the middle. If you tow a lot, leave it on a tow tune. A 2% loss is fuel economy is nothing compared to burning up a trans.
Over time deleted trucks do generally save on fuel, but its almost never gonna be a MASSIVE gain. Not having to burn fuel to regen WILL save fuel.
These trucks do actively "learn" as we drive them, when you tune a truck that memory is typically wiped. Its also a bad time of year to talk about fuel economy, winter fuel really skew's the numbers.
On to the millage losses over time, welcome to the maintenance woe's of owning these trucks. There is a lot of really heavy components that all need to spin freely from the motor to the wheels. All of it wears over time... Thats also why people who tune a truck with higher hp tunes tend to start "having problems". At 100k miles there will be things wearing out, all that does is add stress farther up. Tires, brakes, fluid maintenance, bearings, ujoints, accessories bolted to the motor (ac, alternator, etc)................ The list goes on. Loss in fuel economy is the %1 thing that indicates its time for maintenance. If you noticed a drop in fuel economy before tuning, the delete probably isn't your "fix".