Yes we have had canonical problems that were sorted out when Big Daddy was first introduced.
For the first month we had a perfect indexing with pages in dam near perfect order. Then suddenly POP goes the index and we are struggling again.
At present we are homepage only plus 60 supplementals most of which are genuine supplementals but not all.
MC has promised me a fix at next crawl but we get crawled every day and have seen little change other than the number of supplementals increasing slightly.