Yes, the problems you are having come from CloudFlare, not Admin Tools.
There are two reasons to use CloudFlare. One is speeding up the delivery of static content which makes sense if your site's primary content is in a primarily big, immutable, public section.
The other is the protection against DDoS (distributed denial of service) attacks. This is, however, what is causing problems with your site. For whatever reason CloudFlare's DDoS protection gets triggered.
Most likely you should configure your site so that your administrator backend does NOT go through CloudFlare. I believe CloudFlare has documentation on that. I'm afraid I cannot help you with that since it's beyond the scope of our support.
Regarding your question, Admin Tools is protecting you against a different class of attacks. It cannot protect you against DDoS attacks. There is no way for software running on the server being attacked to mitigate a DDoS attack. By definition, by the time you handle all requests you can be taken down by a DDoS attack which simply drowns your server with requests. Therefore the answer to your question is no, Admin Tools cannot substitute CloudFlare's DDoS protection and CloudFlare's DDoS protection cannot substitute Admin Tools' Web Application Firewall. They are two very different things with different scope.
Nicholas K. Dionysopoulos
Lead Developer and Director
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