Is there any way to replace the programs logo with the morrowind logo?

You don't need to run FPS optimiser everytime you run Morrowind. Just set it up once, and launch Morrowind normally.

But, for future reference, here's how to do it:

• Right Click
  
• Properties
  
• Change Icon (near the bottom)
  
• Find your Morrowind location, and click on "Morrowind Launcher".
  
• Select the Morrowind Icon.

Are you sure? I didn't know that.

That, or my computer is possessed. I use certain features of FPS optimiser, and I never open it.

It might be possessed. :shrug:
I'm pretty sure you need the FPS Opt open during gameplay. No need to launch the game from it, but it needs to be running.