From Steve Endow, Dynamics GP 2013 appears to still have bug in Payables EFT CTX File Format.
Dynamics GP Land: Dynamics GP 2013 appears to still have bug in Payables EFT CTX File Format
Payables & ReceivablesInstall, Upgrade & AdminGP 2013
Archived post from 2013. Dynamics GP and the links it points to have changed since; check current documentation before relying on version-specific steps.