Cleanup only catches skills with the exact same name. If two entries are really the same skill but named differently — "AJAX" and "Ajax scripting" — use this instead: pick the other skill, choose which of the two survives, and confirm. The surviving skill keeps its own name, absorbs the higher of the two proficiency levels and any evidence links from both, and takes over every experience link and approval-history record the other one had. The other skill is deleted entirely once nothing points to it anymore.
Still stuck? Report a bug or request a feature.