the error is because the host has it set up already you just need to have the server read the new BigDig version. and with 1.3.9 you need to start a new world sadly since IC2 and some mods are removed.
http://pastie.org/8046959
idk what is happening with 1.3.12 I didn't had this error... but when I try and downgrade it's giving me this error....
I also have MCPC+ #503 should I update?
Use MCPC+ instead that one you have to remove the mods/coremods first and have the server read that file instead of BigDig.jar and then re-add in the mods.