Same note playback issue

When playing back my pipe organ score, if two of the same note are played at the same time and one note is shorter than the other, the shorter note takes precedence and the longer note also stops playing when the shorter note ends. My best guess is that there's an issue with some function that stops the currently played note and doesn't account for two of the exact same note being played simultaneously. The issue also persists across staves, so playing middle C at the same time on both staves will still cause the issue.