clusters use shared disks, there is only one copy of all the databases, connect to them using the virtual sql instance name (thats why its called virtual, it sits above the physical nodes)

Have you updated the .ini file to the virtual name? You will still be able to connect to SSIS using the node name of the live node, but you should be using the virtual name.

Leave the .ini where it is and on each node with exact same settings.