The most likely case is that the si_invoices owing field has been zeroed out. You can set this field to 1 in records to force SI to recalculate the owing field for display purposes. It will also allow you to do payments from the invoice manage screen.
This slows down processing as the owing value is recalculated for all invoices; paid off or not. If you enter the edit screen for invoices with payments due and save them without making changes, the owing field will be properly set. If you does this for all invoices that are outstanding, you can then change all those with an owing value of 1 back to 0 so they no longer force the recalculation.
You can use phpMyAdmin to set the owing field to 1:
UPDATE si_invoices SET owing= 1 WHERE 1
Later you can use phpMyAdmin to set the owing fields with a value of 1 back to 0:
UPDATE si_invoices SET owing= 0 WHERE owing = 1
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