Hey, welcome to PPG,
The mod doesn't change the vanilla game kidnapping plot anyhow, no. Do you have another Nalia-related mods installed? Not de'Arnise romance from pocketplane.net, but another Nalia romance, perhaps?
Other than that, I'm afraid I don't know. Try reloading or try playing the Isaea plot in another area - Promenade, for example. Also, try restoring a clean installation and continue your game(see this topic:
http://forums.pocketplane.net/index.php?topic=17555 ).