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Ah, that's it.
Thats actually pretty trivial. Sorry to have bothered you. As I said I'm new to this i didnt realize the role jack played in this and that it has its own fixed sample rate.

The loop's samplerate really was different from jack's. Now i use the same sample rate and got rid of any phasing and stretching problems.

I dont know if the repository version was built with libsamplerate support, but mine was not. So if libsamplerate is used the audio clip is dynamically resampled for jack?

It still seems as if there is something missing at the beginning of the sample but now i realized that only happens at the beginning of playback. If I place the playhead a bit before the loop it does not occur, so I think this is also a problem with jack playback or my audio hardware or whatever. But I think this a minor issue, anyway, because it seems not to affect the exported song and it is not as bad as the stretching.

Thanks for your help.