The giveaway had to do with the running lights I believe.
Can't be that, as the running lights can be seen in operation on the 2ft in Pen Pals
Did the 2 footer actually appear in new footage much after the second season? I seem to remember most of the new shots being of the 4 footer.
The 4ft didn't debut until The Defector
, eight episodes after Ensigns
. So if they needed a small scale Enterprise, it was all they had until then.
There's another way to know it's not CGI. Just watch the shot in question. Often times with the model work, the hull pass would be cropped ever so slightly differently to one or more of the lighting passes, so at the edge of the frame you would see the lights where there was no hull or vice versa. And that happens on this shot. There is visible space where only the lighting pass is visible and the hull element is cut off.
That said, it still looks like crap and I hope it is replaced in S3. Which is what TrekFan was saying originally.