I was getting the error: "Recently an error occurred while creating the CSS / JS minify cache: A group configuration for "include" was not set."
I'm using NGINX + APC + PHP5-FPM + VARNISH. The error disappeared after I changed the following setting in apc.ini (/etc/php5/conf.d/apc.ini)
apc.stat = 0
apc.stat = 1
Basically this tells PHP/APC to check for files changed every time the code is compiled. This also affects saving settings in W3TotalCache (with the stat=0 the settings don't save).
I'm not entirely sure if the problem is fixed, but the message did disappear after making the change in apc and restarting apc/php and clearing cache.
Hope it helps.