Hi there @Cart ,

Welcome to the Community.

I noticed that a Support ticket was opened with the same information and our Support team was able to find additional info that was missing from this post. To provide info to those who might face similar issues, here is the solution:

After you set everything live, you back-populated your Flow.
 
When you backpopulate a metric-triggered Flow, profiles will enter the Flow based on when the metric was triggered for them.
 
So, looking at your Flow, depending on how long ago someone last Started Checkout, users will enter at different areas, but will always be seen in the Conditional Split.
 
In this situation, you can see the large number of splits not reflected in the individual messages, but if you click further down on the Update Profile Property, you'll see a large number of profiles have already hit this step, even though it isn't reflected in the previous messaging:
 

 
If you add up all of the profiles in the waiting status, subtracting those who previously failed the Flow Filters, you'll find the numbers are accurate.

Thanks,

Alex