So more detail.
The PC had one HDD. It had 2 partitions, an OS and a Data partition. No multi boot. This setup caused me zero eye strain.
I started having (non eye related) issues, so I bought 2 new HDD's. Cloned the data partition to one of them, and the other I installed a fresh Windows 7 on. The nice thing about this setup is that I can just swap the SATA cable and boot up the old setup anytime I want, so it's easy for me to compare each setup to each other. I've been going back in forth, taking pictures of the settings and comparing the two.
Everything on the new install is identical. The PC is the same. The video card is the same. The monitor is the same. The cables are the same. I literally didn't put a finger on anything except the hard drives and some SATA cables.
Both copies of Windows are updated to the exact same update level. Both have the same ESU updates installed. The video driver is identical on both machines. I check the video card system information, it's all identical. I checked device manager, in both setups, all identical. Every driver is identical (chipset, Audio, LAN, you name it). The monitor driver is identical, the color profile is identical, it's all the exact same. Color depth, identical. Every single video driver setting, identical. Every monitor setting, identical. Same Windows theme. Same desktop color. Same icon settings. Same software installed. I even used the same DVD to install each OS.
So it HAS to be an OS setting that I made at some point in the past that I haven't made here. another thing I discovered that points to that, if I RDP into the new setup, from a laptop that doesn't give me issues, the RDP session instantly causes eye strain. So it has to be some OS setting. I just for the life of me can't find anything else. I just ran the ClearType Tuner even though I turned off clearType and that didn't do anything. I can tell by looking at the new system that it is much brighter than the old system. Even though every single setting I can think to check is identical.
Any ideas of what I could have missed? It's not as urgent since I have since just gone back to the old HDD and fixed the original problem so I can use the computer pain free now. But it is very curious.