I managed to narrow down the cause.
When you recast Summon Bone Golem while one already exists and it has the node “Marrow Eater”, the “Awakening Presence” stops working until the player relogs.
The bug was possible to consistently be reproduced and once I removed the “Marrow Eater” node, re-summoning the golem stopped disabling the “Awakening Presence” node.
I believe it didn’t matter whether or not the golem was currently affected by the armor buff during the re-summoning, though I only tested it once and in hindsight didn’t wait long enough to be certain that it had worn off.