This problem has also has been pointed by @moloko in other two topics. There are workarounds, but not full on solutions. Some of it seems to be intended behavior, as stated by taktik in how the processing works (the fx are applied over the raw sample and then repitched, so if you have finetuned the sample before applying dsp the output will sound different).
What I currently do is use RollingSampler for everything… I don’t even touch the “render fx” and “resample” buttons in Renoise anymore. I just hit play and then drag and drop from RollingSampler to Renoise.