With the ability to copy I can paste the texture directly into an atlas and leave the plugin in standalone mode. V3 and V4 for me also always crash when I exit so it avoids this.
At the moment I'm creating 512*512 textures with 4 256*256 textures inside for both diffuse and bump. When you apply the plugin exits and I have to go back for the other channel.
Copy would mean I don't have to actually have a separate image for for each filter forge texture as I just use paste in place to put them on the atlas.
Also added below the error I get when I exit the plugin or stand alone app. Windows 8.0 x64.