I assume that the map project has a reference to the custom functoids DLL or to the custom functoids project. Is that reference set to Copy Local true or false? If false, try setting it to true. It seems like the map build should be satisfied if it can find the dll in the local bin directory during the build. You can probably test it on your dev machine if you just delete the functoids dll from the Mapper Extensions directory then rebuild.
Thanks,
Tom
Thanks,
Tom