Following this thread ( Guild hangout boss reward - General Discussion - Tree of Savior Forum) I finally found the reason why you don’t get the 1M silver reward after killing a boss.
To get the reward, you need to complete “Miscellaneous Quests - Guild Foundation - Repeatable” quest with your guild members every week. Each boss/mission/blockade raid awards 100 points plus 5 points per mob killed during the raid. To complete the quest, 200 points are necessary. Once the quest is completed, you get access to the 1M silver reward as well as 120 guild contribution points. You get neither of these if the guild quest was not completed the week before (when for example you only do one blockade raid which is usually only one boss kill at gives 105 points for the three guild mission entries you have each week).
Hope this helps those who faced the same issue. Just ask your guildmaster to do a Pantorex run for example with one guild mission voucher after you do a Baubas/Boruta/Giltine raid to complete the quest and get the rewards.