Computer Lagging

I recently built a new computer and it seems to be lagging on me. My CPU usage is very low (below 50% from what windows task manager tells me) and I'm using only approximately 1/4th of the RAM

However, these lags only occur when my computer is encoding stuff (for example, using XVID compressor on a fraps recorded game). Even opening the most basic apps such as microsoft word or loading webpages are delayed and/or show up with a Not Responding popup

I've been suspecting lately that it's my hard drive that is causing my PC to lag. Could it be that the workload (the writes and reads) on my hard drives are too much that it causes it to lag? Or could it be some other hardware component that is defective?

My system specs are as follows:
Intel i5-3570K
Corsair Vengeance 16GB 9-9-9-27 1.5V
Western Digital 1TB 7200RPM as main drive
Western Digital 320GB as secondary drive (pulled out of old acer computer)
Antec EA-650 Green

edit: the lag can occur when i'm copying a huge file (over 100GB+) from my other hard drive to my main hard drive (before i compress it with virtualdub). or it could be as simple as when i'm burning a dvd or creating an iso image from a dvd
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  1. is there anyone that can help me with my issue?

    I also notice my computer freezes for a while when i finish downloading something on my firefox and it's at the "scanning for viruses" part. right when it reaches that part, my firefox freezes and becomes unresponsive for a few seconds. this did not happen before

    and i was using this program called WinSCP and it also seems to freezes. It acts as if i have hundreds of icons to load, whereas i only have less than 30. this also did not happen before

    could this be a software issue or hardware issue?
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