>That's part of the driver for the FETs. I can post that part of the
>circuit too, but I think it is unlikely to be part of the problem.

Actually I think that is precisely where your problem is. The bottom FET
will switch faster than the top one in the totem pole, because you have a
capacitor on the gate of the top FET, but not the bottom one. Hence when the
top one is on, bottom off, and you swap states there will be significant
shoot through current while the top one turns off.

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