Thanks for your help guys. I think I’ve figured this one out…
I used an application called MediaInfo Mac to find the frame rate of the footage on the DVD (25fps), then specified that exact frame rate in Handbrake and set it to constant rather than variable. From my research online the ‘Same as Source’ frame rate option in Handbrake seems to cause problems for people.
Hopefully this will be of some use to anyone who encounters the same problem I did.