Thanks to an insightful comment, I have managed to fix my problem! It was either spread spectrum or the d.o.t. (overclocking) technology by MSI. Disabling these settings in BIOS helped me get a way better setting (some milliseconds difference) -- now ntp and adjtimex work without warning about +/- 500ppm!
https://bugs.launchpad.net/ubuntu/+source/adjtimex/+bug/553237/comments/11 https://bugs.launchpad.net/ubuntu/+source/adjtimex/+bug/553237/comments/12 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org