This is just a possibility that I would like you to consider. Many analog to digital converters have jumper selected filtering for 50 or 60 Hz. You would naturally select the filtering "notch" based on your line frequency. A VFD, ramping down would be steering the frequency of your potential line noise source farther below the center notch frequency. Of course, if you really had a phase controller, instead of a VFD, noise would be through the roof. You might ask them if they have different model #s, jumper settings, programming, Et,c. for 50 and 60 Hz. If so, there might be quite a challenge, like an active tracking filter, required.
Good luck,
Joe