It may have something to do with sorting of the slides. Can you please create a support ticket and attach the PP document there?
> ...notes to the slides were all separated from the slide content.
This is still the case it seems. Is it a bug or a design choice? Wouldn't it be more logical to have the content and the notes collocated?
With PowerPoint files, the text is quite often imported to CT in random order. For example, this morning I have a file that contains 16 slides, and in CT's editor the text starts somewhere in the middle of Slide 14.
(I don't have this problem with Studio... the slides and the text are imported in the right order. So for now, the solution is to open the PowerPoint file in Studio and then to translate the created sdlxliff file with CT.)