Most likely, it is because the customer has been placing orders under a different account. Look for duplicates of the customer, and combine them if needed. Shoot an email off to repeat returns (Dana@repeatreturns.com/ Shelley@repeatreturns.com) to see what their point balance should be, then, you can manually add points to the customer by clicking the "Rewards Options" button in the Customer Information screen.
From there you can manually add the needed points.
As a side note, you can also remove points by putting a "-" in front of the number.
If there isn't any duplicates, go into the Back Office -> Configuration, and click the "Download Arrow Rewards Customer" button, going back about a year. Run the download, and check the customer point balance again. If there is still nothing, contact Repeat Returns to see if there are any issues with their account.