I just had that same problem a few weeks ago when downloading a new tune to my 08 R3T. If you do a search on "fuel gauge issue", you will find the thread. If you ride for a few miles it may begin to register but may not register to the full mark. Mine would only register half full.
To correct the problem, I reconnected tuneboy and "created" a failed download so I could reload the base map, then reloaded the desired tune. To create a failed download condition, just unplug the tuneboy cable while downloading a tune.
After going through this procedure, I finally got the fuel gauge registering full. I am still not convinced that it is working properly however. The fuel mileage when just running around town seems to be quite low. On trips, I register 40 to 41 mpg.
My dealer contacted Triumph, they suggested the clutch switch could be bad. If you pull in the clutch, the switch is engaged causing your fuel gauge to no longer update. This is done so that when you are starting and stopping, the sloshing fuel in the tank, does not give you crazy readings. The clutch switch is not my problem and the dealer has ordered a new sending unit from Triumph. There was no indication from Triumph (to my dealer) that they ever heard of this problem before or there is some sort of fix coming.
BTW, I was using Tuneboy to download, not TuneECU. Do not know if that makes any difference or not. I am not familiar with TuneECU.
Thinking about this while rereading my post, it does seem as if the fuel gauge is not getting updated correctly. When on trips, I refuel and the gauge says I have 206 miles to go before empty. When driving around locally, after a refill, the gauge will then read 150 to 160 miles to go before empty. Getting 41mpg on the highway and 30 mpg around town, does not seem right to me. I was not getting that large a variance before the download that seemd to be connected to this problem.
Keep us posted on what you find! I will do the same as I learn more.