Preserve the formatting of the command window
Pasting the contents of the clipboard loses all formatting - msbuild (and other programs probably) format (colourize) their output which makes them far more readable but only while it's in the command window.
Preserving the formatting when copying would provide the same benefits in the event the command output is copied and pasted to a file
Check the "Command Prompt" Properties dialog, "Experimental" tab, "Filter clipboard contents on paste" to see if that's what's breaking it or can fix it for you. Sure do hope that tab's not going away after the experiment is deemed a success.