Link rel=canonical not working - according to WMT?

[agent_x]

Is anyone else seeing this in GWT? Suddenly I apparently have duplicate titles and meta descriptions on a couple of sites, because Google seems to think the default homepage "/" and "/index.php" are now two different pages even though they both have the "link rel='canonical'" in the head section, and have done for the last couple of years.

[tedster]

I am not seeing this across scores of websites - however, most of them also use a 301 redirect to point index.php to the domain root (or folder root) and they also use only links that point to the canonical.

When you look at your actual Google traffic, is it being sent to both URLs or only the canonical? That would be the big indicator that the canonical link isn't working as intended. Other than that, it could just be a WMT data problem. They've been know to happen ;)