I've tried the following.
1. Ran AutoHotkey script as administrator.
2. Enabled the Add 'Run with UI Access' to context menus option in AutoHotkey Setup and also tried running the script with that option.
3. Ran the visual basic program in administrator mode.
4. Turned UAC to lowest setting.
5. Verified the control names did not change.
6. Yes, we did reboot the computer.

The interesting thing is, ControlGetText can read text out of the edit fields, but cannot write with ControlSetText. These are fields that can be typed in so questions on that is not an issue either.
In the past, any issues I had that were suspected as UAC would be 100% working or 100% not. I am completely out of ideas as to why it appears to work on some commands and not others, on the same Control (ThunderRT6TextBox1) in the program.
Any help on this is highly appreciated. In a few months there is no question I will be moving to windows 10 on my machine. Unless we can get this figured out, it's doomsday.

Thanks.