WMT reporting duplicate content despite URL Parameter settings

[smallcompany]

I thought I resolved this long ago since I was able to enter URL parameters in WMT.
But, since few days ago WMT is reporting duplicated pages for such URL:

example.com/folder/?parameter
example.com/folder/

When I went to URL Parameters and checked "Show examples" G showed only those like

example.com/page.html?parameter

No examples with slash?parameter. Should it matter? I would think G is good enough to figure this. Why now suddenly this does not work?
My parameters were there since the inception of this feature with no trouble.

Do you see the same?

Thanks

[deadsea]

Which section of WMT is showing this message? My guess is under Diagnostics -> HTML Suggestions, but I'm not seeing anything like that there myself.

[smallcompany]

Which section of WMT is showing this message? My guess is under Diagnostics -> HTML Suggestions

Right.

[suzukik]

The reason will be HTML Suggestions are created before Google handles duplicate content.
You can see the detail here:
GWT URL Parameter handling not recognizing rel=Canonical tag ? [productforums.google.com]

John Mueller says:

The HTML suggestions are based on content that we've found while crawling.