I actually stumbled on this by accident. I hit some keys and it selected a part of my timeline and then I couldn’t get it ‘unselected’ or ‘deselected’ so I could export the whole video. Turns out its a simple keyboard shorcut.
My screen looked like this:
with a blue portion of the timeline ‘selected’ or ‘highlighted’. What I had done was accidentally press the keyboard shortcut
"I", the letter “i“. This selects part of the timeline, or creates a “Mark In Point”. You can also do this by clicking Mark -> Mark In Point.
Now, to get rid of this, simply type
"control+z", or select Mark -> Clear In & Out Points.
By the way, Screenflow is an awesome inexpensive video editor.