I assume you by DN you mean hostname. Using just the DN would default you to a specific host depending on the protocol used: http -> 80 -> www, smtp -> 25 -> mx
This sounds like an issue regarding DNS setup on your machine.
When you search using just the hostname, your machine must add the domain suffix which has been configured on your machine. If this does not produce a result, then it will iterate through the other domains listed under your search domains. It is this iteration that takes time.
By using a FQDN you are providing a precise uniquely identifiable address so it will be quicker to resolve via DNS and access.
If you are using Linux, take a look at /etc/resolv.conf
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