Is there any possibility of implementing a sector alignment feature in the FB2K converter when converting to 44.1 KHz/16 bit WAV/lossless?

I have a recording of a concert I made that was filmed on a Sony HandiCam camcorder. When I transfer the video to DV-AVI on my computer using WinDV and use VirtualDub to extract the audio information to a WAV file, the resultant file is 33.2 KHz.

There are basically two options. I could convert the file to 44.1 KHz before cutting it into tracks to make sure the tracks are sector aligned, or I could leave the audio at 33.2 KHz when I cut it into individual tracks.

The latter makes more sense to me because it prevents possible problems with a flawed conversion and it also to saves quite a bit of hard disk space. However, if I want to convert those files to 44.1 KHz WAV at a later time so I can burn them to CD, the 44.1 KHz files are not sector aligned (I run shntool -fix on them to change that). There might also be other problems I'm not aware involving the resampling process in general affecting the gapless-ness of a recording?

There have also been times when I have made a playlist for a mix CD in FB2K (all 44.1 KHz FLAC) and converted it to WAV without resampling to still find the 44.1 KHz WAV files are not sector aligned. My best guess has been that I had a track or two included that came from a live recording that was not cut on sector boundaries that was throwing off the tracks following it, but I'm not really sure.

For both these situations some kind of sector-align feature in FB2K's converter would be perfect because I could create WAV files ready to be burned to CD in one easy step. I'm guessing that it can't be done as a DSP, though, so it would have to be implemented by Peter (not sure if the source for that component is open, and therefore whether or not a third party could implement such a feature).

If I'm making any stupid assumptions, feel free to set me straight. And if there is a way to work around this somehow that I've overlooked, I'm all ears. Any comments/opinions?