Middle-click paste is one of X's many usability fails, especially since it's a convention adopted by no other UI. All the rest assume a max of 2 essential buttons.
Command-C and Command-V are just so much better. Learn to love them.
I don't know the implementation details behind this, but it also seems to me that Ctrl-C/Ctrl-V has a separate clipboard while middle-click-to-paste pastes whatever is selected. Makes no sense to me but I've tried to Ctrl-C / middle click and had issues before. Just one more thing that makes it worse.
