When the EMS says bad ground, what it really means is that ground is not bonded to neutral. It has no way of determining if the ground (and bonded neutral) are at earth potential or not.
Portable generators generally have floating outputs, with the ground not being bonded to neutral. Time2roll said it well; you can either bypass the surge protector with its little switch on the remote (and trust the generator to put out decent power), or else make a bonding plug to also plug into the generator and bond neutral to ground.