I had a similar experience with my Kabinet. In the last two weeks i hat the opportunity to have 4 rehearsals with two bands in two different sized rooms. In both rooms i had that same problem in the beginning: The sound was muddy and very indirect or indifferent. I had to turn up the volume to a much higher level, than usually. My solution to this problem was simply to put the cabinet on keyboard stand in order to make it sound more direct to my ears and to increase the mid and the high frequencies just a little bit and to turn down the bass a little bit as well. I also try to keep the distance between the Kabinet and my ears low, not more than 2 m. That helped me a lot!
Since the Kone in the Kabinet apparently has a wider beam than a guitar speaker in its cabinet, it 'fills' the room with your guitar sound much faster and more at a lower volume. In order to get the same 'beam volume' as you were used to by your old guitar speaker, you need to turn up the volume. That make it even muddier. The more distance you have between your ears and the Kabintet, particularly if it is standing on the ground (huge impact), the more you will have of this 'unwanted sound'.
My other experience was the fact, that the Kone definitely sounds different in different cabinets. I have a Kone installed in a Suhr 1x12 cabinet too, which sounds different to the Kemper Kabinet. It has more focus and a stronger representation of the mid frequencies. I have decided to take the Kemper Kabinet for home use and the Suhr Cabinet for the first band. The second band will require a different solution. I'm thinking about replacing the speakers in my other Marshall 1936 against two Kones and use that for the second band.
Hope it will help you.