I’ve read a few online accounts of people having issues running their generators while also using an EMS/surge protector. I can’t say that I understand it, but it has to do with how inverter generators (which are usually specifically the culprit vs. contractor generators) are not grounded. They have what is called a floating neutral- Mike Sokol explains it quite well in this article.
The work around is to use a plug that ties neutral and ground wires together. You can either DIY one using Mike’s post or you can buy one specifically made by Progressive Industries: GEN-PLUG Generator Plug.
My DIY game is strong, but electrical scares me.