For me, the key to successful meridian flips has always been to make the mount settings (either in the driver or the hand control) consistent with the way I'm asking for a flip in Ekos.
For example, set the meridian limit in the mount to something small, like 1 degree past the Meridian. This tells the mount to flip if a GOTO is executed to coordinates more than 1 degree past the meridian
Then in the Ekos scheduler, set the Meridian Flip to take place 3 degrees past the Meridian.
The mount tracks past the meridian, taking exposures. When it reaches 3 degrees west of the Meridian, Ekos issues a GOTO to the RA/DEC to which the mount is already pointing. As Hy says, it's the MOUNT (not Ekos) which then executes the flip.