Very strange and specific issue here. With 1.7.10 build 2, Custom NPCs will not save Transport data (the types of NPCs who teleport you). Custom NPCs saves its data in different .dat files in the minecraft/server/customnpcs folder, including files like dialogue.dat, quests.dat, etc. All this worked perfectly in the 1.6.4 versions.
For some reason, the transports are being reset to a blank file whenever the server is started up. I have talked to Noppes, and he can't see any issues on his end, which leaves me to think it's an issue with the new version of Edu. Could Edu somehow be conflicting with the saving of one particular file that a mod is creating/saving on its own? Or could it be a Forge issue?