This computer should be able to run the mentioned programs. There are a number of things that could be causing poor performance. The first thing that comes to mind is what type of Antivirus are you using? Some antivirus programs will slow system performance, especially with active protection that monitors files actively. Is your computer currently scanning for viruses while you are attempting to run the games.
Other issues could be that you have malware or viruses currently on your system that is taking system resources. Using malwarebytes in safe mode deep scan will help ensure this is not the case. I would also recommend using a secondary virus scan such as Esset's free online virus scanner to ensure that your current antivirus has not missed anything. While it doesn't make sure you are completely clean it does go a long way toward making sure.
Are all of your drivers up to date? Have you attempted running "sfc /scannow" making sure that you have no corrupted system files and running chkdsk making sure there is not hard drive or cluster issues? I know you said it is fairly new but hardware issues are always possible and should be checked out to be sure. Running a program like mem386 to test the memory is not a bad idea either.
Making sure your network drivers are also up to date, using something like speedtest.net to make sure you aren't having internet speed issues are also recommended.
Other than that without observation it is really difficult to put a thumb on it as like I said there are a large number of reasons, the ones I have mentioned are just some of the more common.
Hope this helps
So this computer I bought recently has been giving me significant fps drops and stutters in games and programs that it should theoretically run well. Any ideas? (IE: TF2, Batman Arkham City, Counterstrike: Global offensive, Minecraft)
Windows 7 64 bit
Two Nvidia Geforce GTX 465 Video Cards. One dedicated to PhysX.
AMD Phenom II X4 955 processor