The boy who went magic / A. P. Winter.

Enhanced descriptions from Syndetics:

A rip-roaring fantasy adventure from a young debut talent about an ordinary boy swept up into a secret world of magic, in the vein of Tuesdays at the Castle ! Magic doesn't exist in Bert's world... or does it? The mages of Ferenor were outlawed and destroyed by the royal family centuries ago for performing incredible feats and powering wondrous machines with their magic, and the world is a much duller place. Bert is a young boy who's lived in an orphanage longer than he can remember, with no friends and the most ordinary life. He's told that magic is just a myth. But then a chain of strange and inexplicable mishaps causes Bert's life to spiral out of control -- only to be rescued by Finch, a plucky girl-adventurer with metal legs. Soon the two are sailing across a sea of clouds with the mysterious Professor, pursued by a royal prince who's desperate to get his hands on Bert at any cost. For magic is all too real and even more powerful than imagined -- and Bert just might hold the key to bringing it back to the world...