Application.Run is the code which executes your whole program - it's not just a single line of code that that performs, it's a huge number!
You need to start logging what is going on in your MainForm - start with the constructor and the obvious Event handlers Load and Shown. The idea is to "narrow down" where in yoru code the exception is being caused, so at its most basic use File.AppendText
] to add "I got this far" messages to a file so you can review after teh crash and work out where it didn't get! When you know the rough area, you can start to focus in using more detailed logging statements until you get it down to a reasonable chunk of code.
Then you can start working out which folder is missing, and why.
But we can;t do any of that for you!