A Myster-E

I dont think its a Yamaha thing, both my EX alto, and my 875 tenor play the alternate's easily. However, alternates are just that....alternate fingerings to help facilitate easy movement between certain notes. Throat position I have found is sometimes key in maintaining a tone that is similar in quality to the main fingering. Working up the harmonic range of the horn can help in this, also, a good exercise that my teacher had me work on was to start on high forked F (alternate F) and bend the pitch a half step to E and make sure it was in tune, then you play the E with its alternate (or regular fingering) and you bend down another half step, and repeat. You do this slowly, with a tuner as you want the pitches to be in tune, as well as paying attention to throat and tongue position on the fingerings and the bent pitches. I used to have the same probelm you are having, but on a vintage horn, and this exercise coupled with working the harmonics helped a ton.