Cross-posting from here, as I'm not sure if this is a Craft issue or specific to the cache-clear plugin.

Intermittently (twice in a day now), I've seen templates being cached with Craft URLs outputting as either /index.php/my-page/ or /index.php?p=my-page

Once this happens, clearing cache via the plugin url (http://domain.com/actions/cacheClear/clear?key=myKey) doesn't seem to fix anything, but clearing cache in the control panel does.

Any ideas?