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So I’ve just recently started playing Eb tuba and am having major difficulty getting the E F F# in the staff in tune. All of them are very flat like 15 cents or more flat. Using alternate fingerings I can bring them close but still flat.
Tuba: Eb Wessex Danube
Mouthpiece: Dennis Wick 2Sl

When I play my Bb tuba I can get those notes in tune.

when I played one of those tubas years ago my first reaction was that the sound was too thin, and the intonation was too wonky. so in other words, it's not you, it's the tuba. First, make sure your 1st valve isn't pulled out any while trying to play those notes. If it is, push it in. 2nd, you might have to use alternate positions. 23, 4, and 24 for those notes.

Have you tried some of the common alternate fingerings? 3 for E, 1-3 or 4 for F, 2/2-3 for F#?

Also, check for condensation? It will affect sound earlier than you are used to with larger instruments. Likely related to thinner sound The sound is also probably still there, it just takes a different touch to drive it.