Carjockey - The most likely response to your specific question is that the difference is perceived rather than actual.
A few things are generally accepted: Longer fuselages arguably tend to "flex" more than shorter, stubbier ones and certainly provide a different ride through the weather. I have worked on a lot of types, and the difference between a 737-300 and a 777-300 is noticeable. The 737 tends to provide a harder, more "seat of the pants" ride, whereas the 777-300 is a more flexible beast. The reasons for this relate to fuselage length and (I think) wing design, not to mention aircraft mass.
The general rule of thumb is that turbulence will be more pronounced at the rear than the front of the aircraft - I can vouch for this from frequent personal experience. A ride that is twitchy and merely irritating at the front can make a hot drink service at the rear a safety hazard.
It is possible that there is some design (or handling) issue that makes the A330 feel different to the 777 in turbulence, but unlikely. It is more likely that a series of coincidences have led you to that conclusion.