I think you are misunderstanding how to interact with themes… the custom profile fields are for the actual profile form… they wont be shown anywhere on the front end other than the form… by default that is… you have to use the sp api to make them display where you want… thats what themes are all about…
why?
well, first you have made the assumption that everyone wants the data displayed… it may be private info only for certain folks, groups or others… so we dont want to assume its to be displayed… we could potentially modify the api to add new data for display or not…
but second, the popup is a single summary of the profile… the custom profile field can be on any profile tab – many of which are not displayed on the popup…
third, where to show it on the profile popup? the popup is segmented into different areas and we have know way of knowing which area the custom profile field is to go into… and since plugins can add new ‘areas’ the complexity of the UI can grow quite large…
fourth, we know nothing about the data being capture in the custom profile field… so we have no way of knowing if it will fit into the size, shape or look of the profile popup…
fifth, and this is the primary reason, and the answer on how to do it… the sp theme you are using actually controls the display of the popup profile… so we, as core, cannot just go adding elements to the profile popup… especially since the custom profile fields plugin already gives you the method for doing this… 
now, absolutely not trying to be critical here – its a great question… I went into a lot of detail because using themes is a big paradigm shift our user base that was used to skins… but basically, its your theme (make your own, dont edit ours), so use the theme to display what you want…
so, back to the plugin… and you can’t really have known this without inspecting the code since we have not yet completed our docs for 5.0 (another reason for the long explanation)… but look in the main plugin file in the custom profile fields plugin… sp-custom-profile-fields-plugin.php
way down at the bottom is a declaration of the template tag the plugin provides for you to add to themes to display custom profile fields… sp_CustomProfileFieldsDisplay()
so then edit your theme’s popup profile template file and add in that call where you want it displayed… ie
sp_CustomProfileFieldsDisplay(‘my custom field’, $spProfileUser->ID);
just repeat for each custom profile field you want to display…
so the moral here is that displaying items is all about the theme…
