This is caused by the explicit setting of LESS which overrides git's default of "FRX" if unset (read core.pager section of man git-config).

Inspecting the OPTIONS section of man less reveals that the "-F" option ("--quit-if-one-screen") is the one that makes less bail out if there is nothing to page and the "-X" ("--no-init") the one that prevents screen clearing ("-R" enables ANSI color code interpretation).

You could either set these globally for less for your user or to prevent interference with default behaviour like with git diff/log you could make a specific alias for syntax highlighted less using something like;

alias lesssh="LESSOPEN='|/usr/share/source-highlight/src-hilite-lesspipe.sh %s' LESS=R less"