Do not convert AVCHD to AVI. It serves no purpose.
Export 25 FPS to match your source, not 30 or 29.97 FPS.
Firstly - The reason for converting AVCHD to AVI is because despite Adobe claiming that CS4 is native AVCHD, the reality is that if I import AVCHD and edit it in Premiere Pro, color correct in After Effects and then render it out from Premiere Pro, I end up with either very significant judder or artifacts in the final result. I stress that this only happens when the input into Premiere Pro is AVCHD, NOT when I use converted (lossless - Lagarith) AVI as my input. In other words, it DOES serve a purpose to convert AVCHD to AVI first.
Secondly - I am NOT using 29.97 or 30 fps.
I am exporting in MPEG2 HDTV 1080i25 (i.e. 25 fps, which is the only available option for this preset), as I wrote in my original post...
The frame rate was the only logical explanation I could think of to explain the shorter duration. If that is not relevant in your case, I'm stumped and you are unique I think.