[Joel]

Would you be able to send in a sample document to omnigraffle@omnigroup.com that's showing these formatting changes? (or attach it here)

We've not seen any reports of text formatting bugs in the 5.4 beta releases so far.

As to your second issue, those objects are set to "Resize to Fit" in the Text Position Inspector, which means the shape automatically sizes itself based on the text inside it.