Sorry, but I don't have an answer or solution for you but maybe a tech guru who's familiar with that Mac will hopefully chime in.
All I can suggest is trying a cold boot after a shutdown and boot up using Safe Boot Mode and see if things improve. To do so, push and hold the shift key when you heard the startup chime, login and try using your Mac. Some things that need extra extensions won't work, but the normal OS X stuff will.
If the problem disappears, the problem will be caused by some third party software.
Activity Monitor (Utilities) may give some indication of the cause if you keep an eye on it when the problem happens, otherwise, it no doubt some hardware problem.
You've got two graphic processors in that machine. I believe one is a nVidia, the other you mentioned is the Intel HD 3000 which is integrated. Anyway, the symptom you described sounds very much like the graphics processor is acting up.