9 yr old has benign acute myositis for the second time in a year. both times while recovering from a virus. could this indicate an ongoing condition?

Less likely: Myositis is a clinical diagnosis based on concurrent viral illness. fever is often associated with it. Acute onset, and recovery. Yes there are several viruses that can cause it, common ones being influenza this time of the year. Confirmation is by doing a CPK-MB fraction assay. Without such information recurrent episodes have to be looked at further.