Hi, A couple of reasons to start with. The RCAF did'nt get a F/E training school until i believe, late 1944, and the RAF had a surplus of F/E's, which is why many went to Canadian squadrons.
A bit more background: when the BCATP was planned in late 1939, there were very few aircraft in the RAF that required Flight Engineers. It was assumed that the UK schools could meet the need. The increase in 4 engined bombers changed that a few years later, but by then all Canadian resources were going into the original scheme of BCATP schools. No. 1 Flight Engineers School at Aylmer didn't open until July 1944, at a time when other BCATP schools were merging and downsizing because of a surplus of trained pilots. It only graduated 1,913 students, out of a BCATP total of 131,552 of all trades.