updated 04:50 pm EST, Wed November 28, 2012
Apple expected to provide new drivers
A fix is in development for flickering on Mac minis connected to a monitor via an HDMI port, according to a post on Intel's forums. "We are aware of the flickering issue, and there will be a fix provided in the future," Intel writes. "The overall flicker issue is also being addressed here; http://communities.intel.com/thread/32932. [Apple] will provide the driver with the fix when they are done configuring our driver (that has the fix). An ETA on this is currently unknown."
The problem -- and Intel's admission of a fix -- would indicate that the problem appears to stem from a bug in the Intel HD 4000 graphics chipset used in the Mini, which is also causing trouble with PCs. To circumvent the flickering, a Mini can be connected using Thunderbolt or Mini DisplayPort instead.