Logic Pro X has many variables that can change the size of the Mix window and this can cause issues with the Alignment of the Raven Internal Mixer. Make sure the Logic Mixer is scrolled all the way to the bottom and the Solo/Mute buttons are directly over each other.
The red line is set for stock Logic setups, so if more than 5 inserts and 5 buses are in the mix window it will need to be adjusted a little lower than the red line.
Raven uses Screensets 8 and 9 to open the Project and Mix windows. So if the alignment is off, adjust it by hand and then Unlock and Lock the Screenset so Raven will recall the correct screen set when switching in-between Project and Mix.
When working on an older project it is easy to adjust the window bounds by importing the Raven Template "Screensets". This Raven Template is installed during the Raven installation and can be found in /Users/Name/Music/Audio Music Apps/Project Templates.
Be sure that the correct items are showing the in Channel Strip Components.
Be sure the Display Color preferences are set to the Top Default Settings.
Note: Changing the Color of the screen can upset the alignment of the Internal Raven Mixer since it is only setup for default screen colors.
Keeping the OSX Dock Hidden will also help the Alignment.
Press the Bank Left 24 button a few times to reset the Raven Internal Mixer and see if that helps alignment.