I can confirm this is happening sometimes. I have changed the priorities of some messages, I don't know if it has an influence on this issue.
I'm not sure it happens everytime, but when it does happen, this is what led to it:
1. Win a war, usually a holy war, and get excess holdings to redistribute.
2. Use character finder to find a suitable new vassal. Often, I like to land genius/quick characters to ensure that they reproduce and maintain a pool of such characters for my dynasty to marry, so this is what I look for in the character finder.
3. Decide to give a holding to a character who is in the council of some vassal. Generally, I give a full county with all holdings and let the IA redistribute. Sometimes even a full duchy. Don't know if the issue appears when giving only a baronny, but I can't see why not.
4. Get a message (pop-up window for me, but maybe due to my custom message settings) saying that new landed character is no longer councillor for *me*, where it should say that it is no longer councillor for *his previous direct liege*, or alternatively, where it shouldn't say anything at all (after all, it's not my council).
Additional details:
-- This happened in a muslim run where I had multiple emperor-tier titles (Arabia, Persia, ...) and where I also held the caliphat sometimes. I think the issue happened both with and without me directly holding the caliphat, but I can't be 100 % positive. I had all major DLC except RoI and SoA, but Sunset Invasion was disabled.
-- This is also happening in my current byzantine run where I'm Emperor of Byzance (only Emperor-tier title) and hold no religious title (obviously, as orthodox characters can't). All major DLC except RoI, including SoA this time. Sunset Invasion still disabled.
-- I am always playing in Ironman, so I can't give a save where I know this will happen and exact repro steps. (By the way, an official statement in the Ironman thread would be greatly appreciated

)
-- Playing on windows 7, latest stable patch, no beta.
Hypothesis:
The message warning that the new landed character is no longer a councilor is sent to the new and current direct liege (the player) while it should be sent to the previous direct liege (a vassal of the player).
EDIT:
-- The OP is mentioning Kaiser, and in both cases for me I was also Emperor. I can't remember it happened while I was only duke/king in the muslim run, and I started directly as emperor in the byzantine run.
-- Since I play in Ironman to get the achievements, I use no mod except "Interface adjust + Keyboard shortcuts" which does not change the checksum string.