Difference in script compilation in BuildStreamedSceneAssetBundle vs BuildAssetBundles

I am trying to port some code from the Unity4 AssetBundle build system to the new one. My goal is to build some scenes into their own bundles. This worked well using

 BuildPipeline.BuildStreamedSceneAssetBundle(levels, outputPath, BuildTarget.StandaloneWindows);

Now, I tried to do the same with the new system, i.e. I added respective scene to a bundle and tried to build it using

 BuildPipeline.BuildAssetBundles("Assets/AssetBundleOutput");

The problem is that I get the following error:

 Error building Player because scripts had compiler errors

The compiler error is:

 Unhandled Exception: System.Reflection.ReflectionTypeLoadException: The classes in the module cannot be loaded.
   at (wrapper managed-to-native) System.Reflection.Assembly:GetTypes (bool)
   at System.Reflection.Assembly.GetTypes () [0x00000] in <filename unknown>:0
   at Mono.CSharp.RootNamespace.ComputeNamespaces (System.Reflection.Assembly assembly, System.Type extensionType) [0x00000] in <filename unknown>:0 
   at Mono.CSharp.RootNamespace.ComputeNamespace (Mono.CSharp.CompilerContext ctx, System.Type extensionType) [0x00000] in <filename unknown>:0 
   at Mono.CSharp.GlobalRootNamespace.ComputeNamespaces (Mono.CSharp.CompilerContext ctx) [0x00000] in <filename unknown>:0 
   at Mono.CSharp.Driver.LoadReferences () [0x00000] in <filename unknown>:0 
   at Mono.CSharp.Driver.Compile () [0x00000] in <filename unknown>:0 
   at Mono.CSharp.Driver.Main (System.String[] args) [0x00000] in <filename unknown>:0 

My project uses some (native and managed) DLLs that work fine in a normal x86 build.

What can generally cause this kind of build error? The strangest thing seems to be that the old-style build works fine, but the new bundle system doesn't.