I don't know of a connection limit. It might be a problem with your MySQL server, so maybe you need to fine-tune it's configuration. Maybe it's also a problem with disk I/O. I suggest you install munin to find out what the problem is.
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Does the new ISPconfig 3.0.4 handle DNS better than mydnsconfig, I know that may be a silly question. but it appears to be the "current" product.
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Both ISPconfig and MyDNSConfig are just frontends to make configuration easier, but records are still served by MyDNS. So the frontend doesn't matter.
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Lastly, does anyone know of a way to cluster the mydnsconfig programme so we can have a single external IP but multiple servers handling the requests?
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Any loadbalancer (such as HAProxy) should be capable of this.