This is a known issue also present in Redux. People have talked about it in other topics. There seems to be a slight phase change when printing FX in the sample editor, not only render selection.
It’s like Renoise doesn’t consider the audio latency before rendering the selection. I might be wrong, though.
Since I couldn’t find a good fix, I’m relying on RollingSampler for everything. I just keep it running in the background to sample stuff from my browser, but also to resample patterns inside Renoise. I just hit play and then copy the selection from RollingSampler window and paste into Renoise sampler, very straightforward.