Being brand new to Noteworthy, I'm shocked that something so seemingly fundamental isn't delt with automatically or at least with a dedicated global command! I sure hope there's another way to solve the issue or avoid it altogether. It was issues like this that caused me to migrate to Noteworthy from Cakewalk.
The bars line up fine. What's wrong is the alto staff notes have many marked sharps flats etc. The soprano staff has none so when the two are overlayed there is misalignment...The note heads are not graphically placed properly on the horizontal "timeline" even though the bars are aligned.