Flutes are not legato
When playing a score, it's impossible to make the flutes sound legato. They come out sounding very jerky, with a clear break after every note. No other instrument has this problem. I believe it's because of this line in instruments.xml, which sets the gate time for flutes to 95:
I believe that line should be removed. If you haven't marked any articulation on flutes, they should sound legato, just like all other wind instruments.