It is impossible for me to know for sure without seeing your theme code but if the theme you are using has not been updated in a while , even though you are using the current version of WP e_commerce then that may be the reason.
You can check that for yourself. For your theme to be able to show the Compare Button it must include these do_actions
in these files
You can check /wp-e-commerce/wpsc-theme/ folder and view all that files in that folder to see if the do_actions are there and if not add them.
Hope that helps.