Flood protection is to protect the server from being overloaded with requests. It doesn't matter if it's from a software or a regulart http requests. If it's a lot and coming from the same ip address, then it'll kick in. One way around it, never done this before and it's depend on their webserver, is to set the request inverval on your software. Like send the request one every 10 or 30 seconds instead of all at once.
Good luck,