Note: when I mention the name of a note in this question, I'm referring to the saxophone pitch, not the concert pitch.
I play the alto saxophone, and lately I've been practicing mostly with a tuner. My instructor recommended that I start tuning to C# rather than G. I've taken the advice and started tuning to C#.
Once thing I've noticed now that I'm playing with a tuner is that, when I tune to G, playing C# sounds really flat. As in, halfway to C♮ kinda flat. It happens the other way, too: tuning to C# makes every other note sound extremely sharp.
When it's tuned to G, every note sounds perfectly normal and in-tune, except for C#. I don't know a whole lot about how instruments actually work, but I would guess it has something to do with C# being played completely open.
Is there a reason behind this? How can it be fixed?