Audio issues with video conversions

I do a lot of converting, mostly MPEG-2 to Quicktime. I use Canopus Procoder Express because it seems to give me better results than QuickTimePro, faster and smaller files for streaming.

Anyway, the audio always comes out sounding “hollow”, like a sort of a reverb. I’ve tried various settings, mono and stereo, sample rates and it always seems the same.

Any ideas why this is and how to fix it?