I must admit that I have never personally experienced noise issues with RTDs on VFD driven motors. (Note that I have wired 1000's of RTDs into VFD driven motors).
What is make / model of VFD? I assume that it is a standard 6-pulse type.
Is there a dv/dt filter on the output of the VFD? (I always install a type TCI dv/dt filter on all LV VFD outputs.)
What type of RTD device (or motor protective relay) are you connecting these RTDs into?
Please confirm the type of instrument cable that you are using (ie twisted-triads c/w indiviudal and overall shields). Is conduit rigid steel or rigid aluminum? What other control circuits, if any, share the same conduit?
What is length of conduit?
GG
ps Note that I have never used "VFD Shielded" cable for any LV motor feeder in a VFD application. However this should reduce the likelihood of any noise being radiated to other nearby circuits.
pps If Skogs suggestion of adding a small cap to the RTD input device does not work, I would then consider installing a dv/dt filter on the output of the VFD.
"I have not failed. I've just found 10,000 ways that won't work." Thomas Alva Edison (1847-1931)