Here's my scenario.

I have a page that was storing something in watchdog, but it wasn't working.

Debugging the site I noticed that the first call to module_implements() which cache the implementation of certain hooks, like watchdog, was being first called from querypath_boot because I didn't have querypath installed on a local dev. Once I installed it, everything works fine. I haven't debugged deep enough, but I believe that watchdog is not really meant to be run on the bootstrap, because at that stage, not every single module has been loaded, and then, it caches the wrong list of modules that implements watchdog.