Is there a difference in meaning when one says, inter-generational organisation and trans-generational organisation
Inter- means "between" or "among". Trans- means "across" or "beyond".
As an example, Wikipedia describes the Panama Canal Railway as both "transcontinental" and "inter-oceanic". It runs across the width of the American continent (though the continent is only about 50 miles wide at that point) and it runs between the Atlantic and Pacific Oceans, connecting the two.
So an "inter-generational organization" would be between two generations. The meaning of "between" is a bit ambiguous without further context; it could be an organization made up of people who are in the gap between two generations, or it could be an organization that exists to connect members of different generations. Most likely, the organization would deliberately define itself or its purpose in terms of "generations".
A "trans-generational organization", on the other hand, would stretch across generations; it would have members from different generations, or interact with people from different generations. This would not need to be a deliberate policy, and might just be a coincidence.