yea I found that my ships have trouble when maneuvering in orbit as well
if I use mechjeb 2.6.1to execute. they wobble and won't go into warp either(-- simple-rocket with a command module attached). however when I reduced the deltaV it got better. if that helps too know.
a simple rover (feline utility)using VTOL straight up np.. will wobble on the way down. it will land but it isn't steady when using mechjeb for land assistance. only the recent 1.3 mods are loaded and ship is centered and balanced for thrust and aerodynamics.