The thumbnail size of gallery images is determined by the number of columns that you select in the Gallery Settings AND the width of the page. It is not affected by thumbnail size set in the Media Settings.
Media Settings affect sizes of images inserted into posts and pages. If you need to change Media Settings AFTER you imported your images follow these steps:
Change thumbnail size in Setting > Media
Install and activate the plugin Regenerate Thumbnails (Plugin> Add New)
Run Regenerate Thumbnails from Tools > Regen. Thumbnails