I agree with kegobeer that the unusually high traffic to the website and the resulting switch to a flash widget probably resulted in that false positive you received. Adobe Flash is like a malware magnet. When MSE detected a change to the website, and that change involved a previously NOT detected flash widget, you and others probably got the warning. Once it was determined there was no threat, no more warnings. Which probably shows that MSE was working as designed, alerting folks to a possible threat and erring on the side of caution.