All raids are timed, around 2 minutes. You need to stay in or near the red circle on your map or the raid paused. Currently the only exception is the wolf hunt because it targets you anywhere in the world instead of your base.
The message should stay up the entire time its ongoing and you're in the area. I'm honestly not sure if the message flashes at any point because you get focused on fighting then when you look back up at the message you can think it disappeared and reappeared just due to how you were focused.