I know this is a really old thread, but for people with similar systems looking for answers, here is some clarification, that Gigabyte mother is not compatible with Integrated Graphics, therfeor the throttling may be down to that.
A new motherboard would be the best way forward.
Also the P-states on AMD APUs automatically throttle down CPU frequency & voltage, whenever iGPU is under full load, this is AMD's solution to stay within the 95w TDP limit using something called APM (Advanced Power Management)
Getting AMSMSRTweaker & changing the P-states if you still experience throttling after getting a new motherboard will solve your problem, but only if you have heatsinks of VRMs as this will increase power draw, resulting in more heat and potential failure of VRMs.
Hopefully it isn't too old to post on this thread.
Link for motherboard comparison:
http://motherboards.specout.com/compare/6197-6238/MSI-A68HM-E33-V2-vs-GIGABYTE-GA-F2A68HM-DS2H
The Gigabyte GA-F2A68HM-DS2H clearly stated as not compatible with integrated graphics.