ipcad doesn't correctly pull the interface ID. Manually setting it in the config file doesn't change the interface IDs that are in the flow information.
Currently, all interfaces are given the ID 65535. Attached is a Wireshark dump of data as sent by ipcad.
Wireshark dump for ipcad
This functionality was fixed in my configuration with the following setting in ipcad.conf
netflow ifclass eth mapto 00-99
I have checked the source, it seems you need to set "capture-ports" to enable. Even though the inline documentation of ipcad.conf states that NetFlow operation is not affected by this setting, the source files say in process.c in function process_packet_data:
Changing the capture-ports setting to enabled fixed the problem, netflow capture included interfaces indexed the same as on the ipcad configuration file.