IIRC,
MeshAnimationData2 has been conceived for characters...
MeshAnimationData - for other objects...
... the difference is that MeshAnimationData2 has two frames with the number 0 and with the same vertexes coordinates... i think, for the better pairing of sequence of different animations for the characters.
***
Added.
The cause of violations of the mesh during character animation (after export/import of character's model using S3D) is to optimize UV-coordinates (vt), S3D makes it automatically... see:
http://www.subsim.com/radioroom/show...&postcount=552
http://www.subsim.com/radioroom/show...&postcount=554
Pak3D does not optimizes UV-coordinates therefore this problem is absent... but there are many other problems...