Hi SuperVGBoy,
Happy Holidays!
I have 6,693 mp3s in my collection. They vary in length from 1:14 to 20:06 minutes (with various amounts of silence or low volume when they start) and all are decoded correctly by the old input plug-in (in_mp3.dll v4.103). If your problem mp3s are encoded properly, maybe it's the output plug-in you're using that is causing your issue.
The out_notsodirect.dll output plug-in (v1.7.8.) has an option to remove silence at the start and/or end of tracks. It requires selecting the proper dB level and several seconds of buffer space. It doesn't work very well for me, so I just accept the few seconds of silence some of my songs start and/or end with. These few seconds of silence do not cut off any part of the actual songs.
The app "mp3 DirectCut" lets you delete (cut out) silence at the start and/or end of mp3s without needing to re-encode the mp3s. I have used it successfully to modify my mp3s that had more than a few seconds of silence at their beginning and/or end.