I've had a few WP before and have hard reset them a couple times. This is totally normal. Applications can be checked manually by just visiting them in the store. It'll give you an update option as you already know. The other non-store applications (like Network+, accessories, etc..) take a day or two to show up as an update. It seems it takes a day or so for the phone to register with MS servers and check for updates. I agree its annoying at best. It'd be nice if there was a button to check for all apps manually like in the W8 store.