Storage check hasn't been doing very well since the 8.1 preview was released.
Try a soft reset to see if it knocks down the amount of memory seen in settings.
I'm guessing settings as seen by storage check is not refreshing in 8.1 perhaps.
This is from Nokia`s Storage Check app which has not been updated for long time
I suspect that it`s not really compatible with WP8.1 and shows incorrect info and only partial app list
Try Storage Sense, it gives complete and correct app list and storage use
Ok, storage sense broke it down with different app sizes. I suppose it looks more accurate. I'll just have to wait for the cyan upgrade to drop before this really clears up I think.