Renoise gets its timing (this will be the same in any audio application) via the soundcard (samplerate and the continues sample buffer “polling” from the soundcard/Jack). We do not use any other HW timers for audio. So to me this looks more like a soundcard/driver/setup problem than a problem in Renoise. For some reason the soundcard seems to skip samples from Jack - if there are really no XRuns with Jack.
You are using Renoise for quite a while now, don’t you? Do you always had this problem? Can you remember at which point this started to happen? You seems to have changed quite a lot of system internals (looking at https://forum.renoise.com/t/linux-tips-on-jack-and-realtime-audio/22897)). Maybe something got broken with your optimizations?
To be sure if its a Renoise problem or not, could you try to replicate this problem with other “Jacked” applications? Maybe this only happens when reaching a certain CPU level…