Recently I got a pretty major CPU and motherboard upgrade. I forgot what CPU I had last but I know it was an i3 but anyway I upgraded to a Xeon 5680 6 core 3.33ghz but Im still stuck a pretty bad vid card, Radeon HD 4600 series.

Before the Hardware upgrade believe it or not I managed to get a steady 45-50fps in nearly all areas and this was with fairly high settings with graphic enhancing mods such as 2k Skyrim mods. Now even on low I cannot even touch 40 fps. WTH can anyone explain this and/or possibly help me fix this? I would be very grateful

Delete your skyrim.in and skyrimprefs.ini in your documents/mygames/skyrim folder. Open steam and make sure cloud support is disabled for the game(not sure if this is even necessary anymore) and then start Skyrim. Choose New Game and it should generate new .ini files. Try that first. Backup your old .ini files as opposed to deleting them if you tweaked them.

Also, there may be utilities that the mother board software package installed to "help" your system, those may cause problems. For example, all the Intel Utilities that get installed on their chipsets. Note, these Intel Utiities are for businesses to control the PC's in their network, disabling or even uninstalling those have no impact other than better system performance.

So, try a strict clean boot:

http://support.microsoft.com/kb/929135

Also, make sure you installed the RAM in the correct slots. Some boards the 1 and 3 (and 2 and 4) are the Dual Channel Pairs, on some boards it is 1 and 2 (and 3 and 4).

When you upgraded your Mobo and CPU, did you do a fresh install of windows, or just overlay the new drivers? You may not get the best system performance if there are old useless drivers getting in the way of things.

I did a fresh install. I got the max amount of ram ( this was a gift from my father and he doesn't really know how to build a gaming pc) So he got me like 36g of ram =/ I will also try to delete the ini like said above and do a clean boot ty for ur suggestions guys.

Np Ram. If that stuff didn't help you can try a total reinstall of the game. I had to do it a few times to solve issues otherwise unresolved. Steam does leave some stuff behind so make sure to manually go through your drive.

Thats the thing I reinstalled it and deleted everything including ini but it still behaves like this. I dont think Ive noticed any fps drops in other games either so this maybe a Skyrim specific problem

What was the speed of the i3? those things are fast as hell even if they are only dual core with HTT, now skyrim does not use anything more than 3 cores... i tried disabling 1 and lost no frame rates at all, tried disabling 2 cores and lost 2-3 fps... tried disabling a third core and lost half my framerates, i did noticed that using 4 cores seem to balance the load only, now having more cores do not help Skyrim... since it ask for more Speed rather than more cores.

In resume, if your i3 had higher speed than your Xeon then there is your answer... in the contrary if the Xeon has faster clock than your old i3, then you do have some sort of issue.

If the game is running fast, like in the 50's for frame rates, then the inevitable frame drops to 20 are quite noticeable. Most people use the Skyrim Sutter Reducer to clamp the upper frame rates so the drops are not noticed. I have mine clamped to like 45 or 48 and the game is smooth as buttah.

^This

Everything else runs smooth on my rig(and I own everything) but Skyrim can be a pest without FPS capper. I cap mine at 59 and get little to no stutter. There are mods, programs etc that can get you the same result. Mileage may vary.