Well, interestingly, I have sort of solved it (still testing it) - but have created a NEW PROBLEM.
Previously, I was loading the mesh with the texture alreay mapped to it - so I was just loading a mesh.
I just did a test by loading an untextured mesh and then loading the texture with the 'alpha' flag enabled then applying it to the mesh.
The new result is the leaves are great - but the purple petals have dissapeared.
This new problem at least looks better than the old problem.
Previously, I was loading the mesh with the texture alreay mapped to it - so I was just loading a mesh.
I just did a test by loading an untextured mesh and then loading the texture with the 'alpha' flag enabled then applying it to the mesh.
The new result is the leaves are great - but the purple petals have dissapeared.
This new problem at least looks better than the old problem.