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Does this issue still occur?
It seems driven by the data provided in the update centers, so investigating the data your Jenkins currently holds about available updates (using a Groovy script) would be helpful here. Run this in Script Console and post the output:
Jenkins.instance.updateCenter.sites.each { println it.id ; println it.url ; println new Date(it.dataTimestamp); println it.data.hasCoreUpdates() } println Jenkins.instance.updateCenter.coreSource.id