Whenever I try going in the chatroom of this one site, I get a message that says "G-Lined: dark flooding"
I tried clearing my cookies and cache, and I'm still getting that.

I was having the same problem about a year ago, but it said "G-Lined: racial comments" instead.
I asked the site admin, and he said he's never seen anything like that before.
I tried going to the chatroom a few months later, then it was working fine.
Now this problem is back, but it says "dark flooding" instead.

Does anyone know what I can do to fix this?

The only thing you can do is to contact that network. The network is the one setting that g-line on you (either automatically or manually). Visit their website and use their contact information to ask them to look into it for you. No one else will be able to help you.

A gline is a global network ban, meaning you are banned from all servers on that network. This is usually done rarely and on most networks only after a vote from several servers. Most networks will gline for only a limited period of time (while a kline -- ban for only one server -- can be anywhere from a minute to until hell freezes over, depending on the discretion of the oper setting the kline).

Clearing cookies and cache won't help you. The message you received indicates misbehavior or other violation of server/network policies. That is something that needs to be discussed, usually via email, with the network authorities.

The most likely reason this happened is because your IP changed, you was giving one with a G-Line on that network.

This has happened to myself a few time. Just follow Riamus2's advice.