I haven't noticed that myself. My guess is you're getting the prompt not because of the codec, but because there is a genuine difference between the clip's properties and the sequence - resolution, frame rate, PAR, field order, etc.
That might explain it on clips brought into existing sequences, but I get a different result when creating a sequence in 5.5 from 6.0,1
Taking the same .MTS file, importing it into project, then creating a new sequence by dragging the clip onto the New Item icon, I get:
Premiere Pro 5.5 - AVCHD 1080i 29.97 fps
Premiere Pro 6.0 - AVC-Intra 100 1080i 60 Hz
Apparently between the two versions of PP, the codec is being interpreted differently. I am not sure what practical effect this may have on things, as I have not moved into any actions or procedures in which this has caused a problem, other than the warning when dropping one of these clips into a sequence that was set for AVCHD.
I see that you're right. I downloaded a couple of clips and tested. Two of the AVCHD clips created AVC-I sequences, and one created an AVCHD sequence. The one that was different was PAL and had 5.1 audio. The other two were NTSC with stereo audio.
I don't know if the frame rate or the audio made any difference, but there it is.
Yes, mine that have been coming in AVC-I in PP 6.0 are also NTSC with stereo audio, so that much is consistent.