I figured it out. Turns out it was my aftermarket batteries. When using some of them, they would throttle the computer down to 0.98Ghz and with some other batteries, they would run at 2.16Ghz sustained. Even though the battery that throttled down to 0.98Ghz lasted longer, it's not an indication of battery health. Even brand new aftermarket batteries do this. I had to find a good aftermarket battery that didn't' throttle the computer and now I'm good. 
For some reason, my computer runs slow and won't turn on the fans when I am using my Latitude D620 laptop unplugged. When it is not plugged in, it throttles down to 1ghz with 40 percent CPU utilization and everything runs slower. But the moment I plug in the charger, it jumps back up to 2.19Ghz and goes back up to 100 percent CPU utilization. Is there a reason why this is happening? I have another D620 and it doesn't have this issue at all. The cooling assembly is clean and there is no dust and I added some fresh thermal paste as well. The fan is confirmed to work as I heard it ramp up during the BIOS flash.  Also I checked the power plans and I am on High Performance. I have already tried removing and reinserting the battery and reflashing the bios but nothing seems to work. 
Dell Latitude D620 Stuck at 1Ghz when unplugged