I agree with the other comment to beware and look at getting a new drive in case this one is shitting the bed.
If it were my system I would look for any signs of disk related errors in the logs (likely would show in /var/log/syslog or maybe kern.log).
Also, did you empty your trash (if you used GUI to kill the files)?
You verified the disk has free space right? (Via df or whatever GUI tool, maybe disks or the file manager)
Another thing I might look at out of curiosity is disk io stats. Is the disk swamped with IO for some reason? We’re assuming the bottleneck is disk io but then again maybe something else weird is going on.