I'm having a bit of a play with iBooks today, and some 3D model stuff. iBooks has, for me, always crashed when displaying 3D models. I don't have a jailbroken iPad, so it's not a DRM issue (at least not one caused by that). To tell you the truth, I'm not sure what the cause is. But, I do have a fix!
That simple. My books and PDF's were still on the iPad, so there was no issue with having to resyc everything. Now, 3D models are supported :-)