Problem with module dependencies

The project I'm working on (an imported eclipse project) has a bunch of modules and there is a bit of cyclic dependency that seems to be causing some problems. Module B depends on module A while module A depends on an obfuscated jar of module B. This jar is being built outside the IDE by some gradle tasks. With this dependency structure, everything compiles fine but looking at the source of files in module B shows tons of red - most all imports and types not being resolvable. But again, this doesn't actually prevent compilation. If I change module A to depend on the source of module B instead of the jar, all these spurious errors go away.