Classpath is inconsistent between multi-project build and single-project build

I’m using ForgeGradle to develop Minecraft mods, and I’ve just tried to use it in a multi-project build (this one). I have no reason to believe the plugin wouldn’t work in a multi-project build when single-project builds are fine. However, it fails with a strange class path error, actually related to fetching resources. Log here (warning, posh is hard to redirect). The author of ForgeGradle believes there is something wrong with the class path, but we haven’t been able to deduce what is wrong.

Note: when looking at the above repos it’s important to ensure you’re on FG_1.2 for ForgeGradle and feature/forge-1.8 for WorldEdit.