I am finding that when I use this command (bound to "." in the org agenda), I often do NOT go to today.
Looking at the code, it seems like org-mode may be guessing today based on text markup: (let ((tdpos (text-property-any (point-min) (point-max) 'org-today t))) We jump to this position, instead of checking the clock, if we can find it. If it helps, I often leave emacs running for days at a time, which I suspect could be confusing it about what today is. E.g., this just happened to me when I tried to update my org-agenda after having been away from it overnight. Perhaps it would be an improvement to look at what we find at TDPOS and check to verify that it corresponds somehow to org-today?