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. There are DIY instructions in Mike’s post.
Here’s a plug from Southwire, a company that sells EMS systems.