Bump, has anyone been able to fix that "issue"? I have a freshly hacked 2ds with that problem - every time there is a CIA installed, the console needs to be rebooted in order to unwrap the gift. And also, as takasu27 wrote: "...when you click to other apps its banner wont show but when you restart the console its ok again".
I followed 3ds.guide, so it's got newest luma+a9lh.
UPDATE: After a bit of experimenting I found out that it only happens if I close homebrew apps like freeshop and FBI by using in-app exit option ("select" button for freeshop and "start" for FBI). However, if I close these apps by pressing "home"->"X" everything works normally (I can unwrap without rebooting and banners are showing).
Is it considered normal or there is a fix for it?