This is proving a bit of a deal breaker for me as I'm having to go back to using illustrator again.
If I group all red objects / text in one layer, all blue objects / text in another layer etc, when I export to PDF and choose 'keep layers', none of the groups are honoured. Everything is just a mess and I have to go back and group them all again. This takes a long time to do as sometimes I have to deal with well over 100 layers / groups. The frustrating thing is that even after I've re-grouped all the objects & text in colours, there's no way to just save the pdf again without re-exporting the document and guess what happens to all my newly created groups on export? Yup, Publisher rips them all apart again and chucks every thing all over the layers pallet.
Not happy at having to go back to Adobe but there you have it.