how do u do your thumbnails? trough admin/auto thumbnails? or when u upload picture as a user and the script creat thumbnail from it?
if u do auto thumbnails from admin panel, after search for pictures without thumbnails it will ask u what size (width) would u like and what compression level u want.
if u upload as a user and let the script creat thumbnail, then u need set thumbnail size in admin/settings (well, this u should do anyway)