I had noise suppressors on the spindle motor leads. These smoked the first time I tried to run the motor with the VFD. I removed them, and the motor and VFD work fine. They smoked because the VFD has a PWM output which has a high frequency component, which these suppressors were designed to suppress, and gave there all doing it. I did need to put a noise suppressor on the input to the VFD. From the other posts, it sounds like your setup is different than mine. I have EMC2 give me a spindle speed value, then a DAC voltage to my VFD, then VFD output to the motor, easy peasey. The VFD has a three phase input, but I cheat, and give it single phase. The only other three phase bit is the flood pump motor, which has its own VFD. My original control power supply ran off of two legs of the three phase. It now runs from the two leads from single phase 240 VAC. It sounds like you have some other three phase stuff? If you have control electronics on three phase, my guess is it gets converted to some other voltage before it gets used. You may have input voltage and phase options on the control supply. My guess, as robh indicated, if this three phase input gets converted to DC, the input diodes and capacitors will be stressed more as you get away from true three phase. Some VFD's have over sized input circuits to allow for three or single phase input. This is mostly me thinking out load, so take it with a grain of salt.
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Kirk Wallace
www.wallacecompany.com/machine_shop/
www.wallacecompany.com/E45/index.html
California, USA