Apparently the error message will persist for up to 1 month (not good in my book) So it makes it more difficult to check when you have an issue and when you have it resolved. Apparently you have to check the License section (which is updated nightly), the current count on Certificates in Onboard (which for me shows more certs than the licensing page)
All in all very confusing to try to resolve the error message - but it does stick around after you have cleared up the license total/used issue