jellby: I can't reproduce this with the latest beta firmware. And, when I hunted through my books for an example that would fit, I found a few books like this. None have caused me problems with the ToC.
But to check, you are referring to the following in the toc.ncx
Code:
<meta content="e03c471a-2c89-4241-986c-e60dcba32256" name="dtb:uid"/>
and in the OPF:
Code:
<dc:identifier id="uuid_id">urn:uuid:499a2178-2c3b-4bce-9f72-03b3be940b3f</dc:identifier>
Those are from a book I have no problems reading with 3.5.0.