Oh, I know. There's a number of problems. I mean, ugh, how damn hard would it have been to make the damn model match the 6-footer? It's especially jarring in episodes where footage of BOTH models are used. Ugh.... TREKKER SMASH!
It's a trade off between the three models. The 6 footer looked best, but they could barely move the thing because of how large it was. The 2 footer could move much more easily, but it looked terrible. The 4 footer was the compromise, and the main reason the ship was able to move more in later seasons.
I'll just say I prefer good models over bad CGI ships any day!