DirectAdmin doesn't touch anything that would make your server unreachable.
FC5 uses yum. Check your yum exclude list against the exclude lists posted on these forums.
However nothing yum updates should cause your server to be unreachable either.
It's possible that your server is plugged into a switch port or router port with an intermittent failure. That would be a data center issue, though one they may not find. If the problem recurrs you might ask them to change to a different port.
We've had this particular problem before, so I know it can happen.
We've also had memory problems that have caused a server to become unresponsive; generally when that happens there's something on the local screen, but most servers don't have a monitor attached, so no one would ever know.
We've had that problem as well.
A motherboard problem could cause the same to happen.
Actually, a stray electron out of the atmosphere could cause it to happen as well, but I don't want to offer you too many options

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Jeff