OpenToonz seems to have separate resolution controls for the Cleanup Processing, Canvas, and Camera.
Since Cleanup Processing is currently not working for most 1.0.1 installations, I would try to mess around with the Canvas and Camera settings. Watch for the DPI settings as well, even though DPI isn't supposed to affect digital projects.
I should note that completely vector based projects do not have a canvas size setting, and are only reliant on the Camera Settings.
I run 1920x1080px, aspect ratio 16/9, 72 dpi...
Until we get OpenToonz to an adequate enough point, I would avoid using it for anything audio related. Use After Effects, or a free alternative video editing program, then align audio within that environment. If, however, you are doing this (b/c I haven't heard of any Audio features as of yet, then there is a problem with the animation's frame rate).