Tweeted this question and got response from @iromeo (Roman Chernyatchik) that the red question marks are represntation of a model on one of the model relationship no having a relationship to the other model.
i.e. Model A has_many Model B, but Model B doesn't have belongs_to Model A.
Unfortunately for me, our models have those relationships.
The quirk is that our main model, the one we created the diagram for, is in a subfolder (.../apps/models/A/<multiple files>.rb) and split into multiple files. This is due to the model being huge. We know this is a design issue, but...
I'm on Build 1347 EAP, jdk 1.5_019