Hi @NickD
How do you mark invoices as paid? Do you tag them from the bank statement, or do you use the “Log Payment” button on the invoices themselves?
In terms of fixing it, I would assume there are untagged transactions which would be duplicates causing this issue. Initially, you would use the recon tool to identify the errors, and it’s just the case of removing any transactions which don’t match your bank statement. There’s more info on the recon tool here: Reconciling your bank