Exporting as MPEG2 DVD or MPEG2 Blu-ray makes my clips shorter!?

Hi,
Firstly - I am shooting footage on a Panasonic HDC-HS300 using the 1080i 25 default setting, and importing the AVCHD file as such into Premiere Pro CS4 v.4.2.1.
My aim is to get the best image quality results possible using a workflow where I take the raw AVCHD footage (possibly converted to AVI first) into Premiere Pro, Dynamic Linking to After Effects for color correction etc, and Dynamic Linking back to Premiere Pro for final export/render in several different formats for several different purposes.
Anyway - Here's the problem:
I have been playing with different ways to do this (for MANY hours), and have found that whenever I attempt to export/render out from Premiere Pro with Adobe Media Encoder using either the MPEG2 DVD or MPEG2 Blu-ray (both using the default HDTV 1080i 25 settings), I end up with clips that are shorter than the original clips! For example, I have been editing a clip that was originally 56 seconds long, but after the export/render it is only 48 seconds long.
To make things even stranger, the accompanying audio file that is rendered out along side the MPEG video file not shortened and comes out as 56 seconds long, as it is supposed to be.
Someone please help....?
Thanks
Mikkel
P.S. If I were to convert the AVCHD to an AVI format, which would be the best applications and formats to do so?

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...

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