On the Feb 14th update, we were given this option:
*Added an option to the Hero Control panel that forces Heroes to drop the currently carried bundle. This option is mainly useful for forcing Ritualist Heroes to drop urns created by skills.
When a hero is holding an item, the target button the left side of their skill bar turns into a "Drop" button. Now that we have this option, there are some anamolies with how Heros handle bundles.
Observing how the Heros handle these skills we can separate them into a number of different categories.
Cast on Attack
Angished was Lingwah - Drops when attacking foe and if no other Pain spirits are in earshot
Blind was Mingson - Drop on attack
Cruel was Daoshen - Drop on attack
Attuned was Songkai - Never drops
Vocal was Sogolon - Never drops
Grasping was Kurong - Drops on attack
Cast on Defense
Generous was Tsungrai - Drops when health is low
Lively was Naomi - Casts and drops when dead ally is in the area
Vengful was Khanhei - Never drops
Protective was Kaoli - Casts and drops instantly whenever activated*
Resilient was Kiko - Casts and drops instantly whenever activated*
Defiant was Xinrae - Never drops
Tranquil was Tanasen - Never drops
Cast Continuously
Mighty was Vorison - Never drops
There is something special to note about the two skills I marked with a *.
When using heros, this is most likely not how you would want to have these skills used. Any time they are activated, they are instantly dropped. To prevent your hero from dropping these items automatically, disable the skill first, and then manually activate it. It's not especially convienient, but it works.
Heros and Bundles - Item spells
Skye Marin
Mujaki
I've noticed similar behavior with monk heroes and maintained enchantments. When Koss was still Lv2, I decided to let him use Mending. But he would immediately deactivate the maintenance. As you found, Shift-Click to disable, then manually force the skill activation, and it would remain.
Metasynaptic
This behaviour with maintained enchants has been around since day one. The fact that item spells use the same logic is not really a surprise.