While the GPU client sometimes run in C> Program Files (x86)> Folding@home> Folding@home-gpu, most of the time the active folder is C> Users> [Your User]> AppData (hidden folder)> Roaming> Folding@home-gpu.
So change the location for the GPU client in affinityinput.txt and it should work out better.
-when installing SMP, I make a folder in the root for it and run it with the -local flag. This puts everything in this folder.
-when installing GPU, I use the console client. I make a folder in the root and run the installer inside this folder; it puts all its files in the folder it's run in, so it mirrors what was done with SMP.
There, same target easy to find for both affinity and HFM