Macbook Pro 8.1 with El Capitan doesn't shut down after last update when Backupvolume is connected.

My Macbook 8.1 with El Capitan doesn't shut down when I have my Time Machine volume connected. The Time Machine volume (500GB) is on a 1TB external drive which has a second partition with 500GB for storage. The Macbook works normal when I don't connect the external drive with the two partitions. However, it does not shut down or suspend when the external drive is connected; it rather attempts to shut down or suspend but keeps working with an already black screen. The ventilation will then work heavily and the computer will become hot. I always have to force a shut down through holding the On/Off button until the Macbook shuts down 'cold'.

This problem has occured after the most recent update for El Capitan. I noticed that the Time Machine volume does work when connected, but the icon for the volume vanished.