If you run into a company who had paid dues, but still shows as having an overdue balance, it could stem from a merge.
For example, let's take at a look at a member's transactions. The company below is showing a sales receipt for a credit card payment for dues of $450. Above that, you will also see that they are showing an overdue dues invoice for $450.
If you notice this happening, check your QuickBooks audit log. The audit record may show that there is a deleted customer of the same name as the company having the issues in Novi.
This is most likely the result of a merge, hence the duplicate transactions you are seeing in Novi (invoice and sales receipt for the same payment).
If the sales receipt is valid (you did receive the money), a fix for this is to void out the invoice.