I've just notice what I presume to be a bug when selecting a note / highlighting style:
When I select the text I wish to highlight, I then change the note file I want to save my highlight in to a different one than that selected when the highlights dialogue box opens. When I then select a different recent highlight style to make my highlight, the note file switches back from the note file I manually selected to the original note file that was selected when I began the highlight process.
This isn't limited to a particular resource or note file, it's happening universally at the moment. I'm running iOS 3.5.0 on an iPad 3rd Gen.
This is annoying because I've only just discovered it, and it's meant that I've got many highlights in wrong files whilst I was unaware this was happening.