I've just completed building a new computer, but for some reason when I'm playing any game every 30 seconds or so I get this 3-5 second fps lag then it goes back to normal. Also, while it's lagging I can hear a high pitched noise coming from the video card. I'm using a BFG GTS 250 OC 1gb btw.
Your probably maxing out your GTS 250 with that 23" monitor and it could be overheating. Manually raise your GPU fan to 80%, leave out case side pabel too, and then start gaming. If the problem goes away, then you know it was a heat issue. Leaving out the side panel will also help you find where the noise is coming from (could be your GPU capacitors, inspect them for deformed end caps)
The sound if not from the fan is the power stages on the card. You should check your cpu usage and psu if the unit is fit for running your card. If the psu is enough or more and cpu is not at full load then there may be an issue with the card. PS I had this problem first had before so just check the hardware to rule out problems there first.
It makes squealing sounds both under load and idle (There's no noticable fps loss when idle). Usually 2 or 4 cores are being used when playing a game. (Left 4 Dead 2).
Do you have the same general fps issue with other cards? Do you have another card on hand to rule out the GTS250 being the problem?
There may be an issue with the card the requires RMA due to the power stage (the part of the card making the odd noises that supplies power to the gpu core). I have fixed issues like this on my own so this one might just be a bad sample. If you have no warranty you can do a simple mod by applying a small heatsink to the mosfets and the choke coils (did wonders on my x1900xt and 8800gtx).