Hi Ryan,
What version of Payables are you using? That may shed additional light on this. Perhaps you are using an older version that has a problem that has since been fixed.
The option for 'Set Amt Payable to Inv Balance' can be found in the Company Profile on the System/Report Options tab, on the right side, about half-way down. If you are using the shipping version 9.2A, the tab name is simply System Options. This feature was introduced in Payables 8.1E in 2012.
If the Max Payment is 0.00 for an invoice, it must be edited to something positive in order to pay it. And the overall total check amount for the vendor must be positive in order to write a check. For example, a 100.00 invoice will not be paid if there also is an unapplied 100.00 prepayment for the same vendor, netting the overall vendor amount to 0.00.
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Regards,
Softrak Tech Support