Ran into this problem tonight, and tested it to my satisfaction. Probably the achievement is based on unlocking all the gates, which get bypassed if you use the shortcut.
I had the same problem twice. The third time it worked.
The two times it did not work, I had left the top of the tree trunk (boss area) to do other things while the countdown continued. The third time I stayed in the boss area on top of the tree trunk and the daily worked. I also took the shortcut worm the third time. Hope that helps.
