A Valve employee posted this about the FPS concern:
Hi all -
Free to Play brought a huge influx of new users to Team Fortress. To help server counts scale up to match the demand, we are reworking the dedicated server for performance. We want to improve player responsiveness as well as to reduce CPU usage so that hosts can run more servers per physical server.
Some of those changes addressing CPU usage went out last night. Server operators should see a big decrease in CPU load and can potentially run more instances per physical box now. However, a side effect that many of you have noticed is that server FPS has an effective cap of 500 instead of the previous 1000, or possibly even lower than 500 depending on your Linux kernel HZ setting. This should not have a noticeable impact on gameplay as the tick rate is still locked (well, mostly locked) at 66 updates per second and the frames that are being dropped are "empty" frames that do not actually run a server tick.
We're going to address this further in another set of performance improvements. Sorry for the temporary confusion, but we wanted to get these CPU load reduction changes out quickly to help with the Free to Play user crush.
Longer term, we want to move away from FPS as a measure of performance and instead show actual load and responsiveness (jitter/latency) statistics. The difference between a tick and a frame is complicated, and fps_max sometimes affects performance in counter-intuitive ways. We would like to retire fps_max for servers and replace it with a more obvious server performance setting. We'll give you all a heads up before we do so.
Before he posted this, I made this statement on Facebook:
In today's Orangebox update, Valve forced its Orangebox games to start running at half the correct FPS rate -- so our 500 FPS servers now run at 250 FPS, 2000 FPS servers at 1000 FPS, and so on. For ultraaccelerated and extreme accelerated servers, a workaround is to double the FPS rate on the "Server control" page, but there is no workaround for Windows servers yet. We are hoping for a quick fix from Valve.
Since further changes are in the works, I'd recommend rolling with whatever Valve wants, at least for now, and see how it all pans out.