Chris, the reason some clips look like they aren’t imported using the Media Browser is that Premiere is correctly identifying which clips are too long and only importing the first clip number of a sequence of spanned clips. For example you shoot a 40 minute clip on your camera which spans maybe 3 MTS files (1,2,3 for example).
Media browser will identify that this a spanned clip and import only #1, but this clip named #1 will contain all the content of 1,2 and 3. This is the right way to do it since it was meant to be one 40 minute clip not 3 different clips.