I can confirm the issue, which is that Eclipse balks on
OuterObject$MiddleObject$Inner because OuterObject and MiddleObject don't
have an InnerClass relationship.  (I'm guessing a bit about why Eclipse
balks.)

Here's a workaround of sorts:

You can create a class called Outer$Middle$Inner in your Eclipse project,
which will only warn on the name.  Give it a stub interface so there are no
compilation errors.

Then in your run configuration, you can "add external jar" to "User
entries" (to add your scala jar) and then move it "up" ahead of the
"default classpath" that includes the stub.

(Alternatively, you can edit .classpath manually, put your scala binary
before java src. The editor will still complain about the classname, but
that error won't stop you from running.)

Is that worth the trouble?  On a real project, the stub class would go in a
special stub-src dir so it doesn't get packaged in product by some horrible
accident.