FlySketch 1.6:

Don’t use PDF for copy and paste.
A problem arises when you use PDF as the format for copying between applications. If you have compositing modes set on your graphics (such as darker/lighter drawing), then that information is lost when sent to PDF. Using the command below, you can skip the copying of PDF to the clipboard, and only rely on the TIFF data being there.

defaults write com.flyingmeat.FlySketch skipPDFCopy -bool YES

Quit FlySketch, paste that in the terminal, and you should be good to go.