Any chance that the HS could have come adrift slightly? No experience with the Mega H myself (Noctua DH-14 at the mo') but I've certainly come across situations where the HS has moved. I also remember hearing that some of the older Arctic Silver pastes could separate if incorrectly stored, but in your case I think that most unlikely that separation is the cause.
Of course, if you've used the tube of "unlabelled white gunk" that came with the HS rather than a
proper compound then who knows. If the case then perhaps this is a golden opportunity to whip off the HS, clean it and the cpu cap and slap on some decent HSC? AS5 is less than a tenner so surely it's a cheap "upgrade"?