The wake timer could be the issue, but it is not the sole issue as far as standby being interrupted because of Windows goes. If you have audio playing or if an audio application is even open it can poll the device preventing standby. (To be clear this is a Windows issue and not a Framework issue.)
But if you closed the lid and the device really drained to 0, something else happened, and I would ask what applications you had open. Something interfered.