The MDR and HDR loads the last song that was opened before shutting the system down. A song that is long, has many overdubs, etc will cause the system to take longer to boot. It is also important to create a new Session for every song. Users commonly record many songs onto the same session, which can bog the MDR and HDR down.
Try creating a new Session, and record little or no audio. Simply save the song, and shut the MDR or HDR down, and reboot. See if the unit boots more quickly loading this smaller session.

Also check for software updates available as free downloads at www.mackie.com