I presume that the vendor in question has an invoice and some other transaction (credit note, pre-payment, etc), that added together nets to $0.00, but individually each transaction still has a non-zero current amount. If you want these transactions to clear to history, then they need to get matched to something and have the current amount equal to zero. You can do this by creating a Manual Check batch entry for 0.00 and non-printing, and apply it against both the invoice and the other transaction. When you post this, the current amounts will be zero.
This may solve your pre-check register issue as well, as all transactions for the vendor will be completed.
If you see the text 'A check will not be printed' under the vendor if you print the pre-check register and do not 'exclude zero-dollar amounts', then this vendor will be hidden with the exclude option selected.
If you do not see this text without the 'exclude' option, then you have a different problem. Perhaps a transaction is dated after your check run date and thus doesn't get selected for your report, or a control payment has been assigned to a transaction to put on Hold. You'll probably have to contact your Adagio consultant if the solution isn't immediately obvious.
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Regards,
Softrak Tech Support