Hi Irvin, good to have some fresh input.
I tested the debugging tool and I get the same message as you. I also looked at the performance tab and I had a little above 140 fps (as I set the fps limiter to 140fps due to my monitor's 144hz) and once I reach the critical spot, where the frame drops, it shows me that it drops down to 25fps, even though its pretty much exactly 3 fps.
Also: When I leave the lagging rocket where it is and go to the space center, the space center is all fine with its 140 fps. I go to the tracking station and it shows me the kerbol system and still everything fine. But the moment I click on the "tracked objects" ship it drops fps to 3 again. if i leave the tracking station all fine again.
So its only with the particular ship that has a bugged trajectory. But no matter how many ships I send into space, every single one has the critical spot. So the only thing I can do now is visit Mun and Minmus...... a lot.... .__.
PS: Also tested it with 1.1 prerelease today, but same...