Do you underuse or overuse your tuner?
Most younger players underuse theirs and never develop a solid pitch center.
Most experience players overuse theirs and neglect their pitch independence. Instead of playing scales with your tuner, try this:
Play the first note of a scale
sing the 3rd while playing the 1st degree
play the 3rd
sing the 2nd while playing the 3rd
play the 2nd
sing the 4th while playing the 2nd
Other ways to improve intonation:
Use a drone pitch -i.e. play a G scale with a constant G playing
Use a recorder for instant feedback on your intonation.
Sing Sing Sing!