Oh wow, that IS something odd! My guess is that FUNi didn't get the other animation sequences, or didn't think to ask for them. Sometimes companies don't get certain openings and endings provided to them in licensing and DVD releases, FUNi had problems before with Dragonball and Detective Conan like that (in the case of the former, Toei didn't give them certain versions, while in the case of the latter, there were rights issues).
I remember they used Italy's MKC in the VOD versions of the episodes with Belarus and Ukraine, did they fix it for the DVD? Whatever happened, maybe we should ask Char about it, but then we'd probably have more luck writing to the Support Team at FUNimation (Char would probably direct us there anyway). Hopefully they'll fix it in a rerelease D: