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Use the Staves and Systems page of Layout Options.
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Select the notes and do Edit > Reset Appearance to undo their MusicXML-obtained properties.
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You can use the various formatting commands in Engrave mode to insert system breaks etc. where you think they should go.
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You can’t manually adjust the distance between staves and systems yet, but it’s in progress at the moment and will be possible in the first post-release update. In the meantime, the options on the Vertical Spacing page of Layout Options are what you’ve got.
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This is indeed a bug.
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If you have problems with MIDI files, perhaps you could zip them up and attach them here so we can look into it.