My server -> has been full since around 8am, however my historical graph shows only 2-3 players online, even now.

http://www.gametracker.com/server_info/198.27.81.161:27015/

From what I can see in your graph,
1. Prior to 8 AM you averaged about 1 or 2 per hour.
2. 8 - 9 AM you averaged about 20
3. 9 - 10 AM you averaged high 20's

The historical data describes average counts over each hour and it does not update immediately. Unless you average 32 for a full hour, it will not show you up that high.

Ah I see, I was at like 20's from 6-7 am, but showed 2-3 players. Also the tracking time is wildly sporatic, it will sometimes scan every 5 minutes, then other times I see "last scanned 38 minutes ago". Any reason for the odd scanning times?

The times are also based on US Eastern time so it may be confusing if you are in California, for instance.

When the scanning times get beyond 5 minutes, it's typically due to the GameTracker scanner being unable to reach your server. Sometimes this is due to anti-flood features in the server's firewall blocking the scanner temporarily. There could be a number of other reasons it cannot reach the server. The GT Scanner has in the past gone down, but we usually get a lot of posts complaining about it and we have not seen any complaints today.

It's not being blocked from my servers, I've white listed your scanning IP's in the firewalls ages ago.