Conservatory student. My scales are in tune; my repertoire is not, the moment a shift or a fast run shows up. Which intonation practice actually carried over for you, rather than just sounding good in the scale itself?
Cellist, same battle. Drones changed it for me - practise the passage against a sustained tonic or dominant so every note has something to be in tune with. Slow with the drone, then remove it. The ear keeps the reference even after the drone’s gone.
Also test the target notes in isolation before the run: find the shift arrival, prove it in tune, then approach it from a few notes back. Most run intonation is really one or two unconfirmed landing notes.