This kind of reminds me of the problem I have with the Ab on my Yamaha tuba I use at school. No matter what, it is always pretty flat. I know it isn't entirely the tubas fault though, since I am still new. Recently we have got it to improve though, after sitting down for a bit and really adjusting the slides, we got it pretty close, at least "hidable" when the other guys are playing.
Although, my friend (former section leader), said that the particular model we have tends to play flat on certain notes often. I'm jealous of my friends Conn.