Strange power problems with PI EMS 30 and autoformer?

Good points above. It's also possible that this CG has lower voltage which is causing the autoformer to boost more often which effects the EMS.

Any time you switch power (autoformer boost for example) electrical transients are created. These can cause unexpected results.

Try another pedestal/CG or even a 25' 30A extension between the two units. And call both companies.

And voltmeter readings might shed more information on the problem.