Could be an app, however I dont think apps have the ability to force the OS to scan the SD card...
I'd hope its a faulty SD card, as the alternative is more than likely a faulty phone. Bit of a price difference there...
If you haven't already, check the SD is seated properly. Try an alternative SD card. Try your SD card in an alternate phone/device.
As a last resort you could factory reset your phone and just leave it all default for a while, see if the issue persists. This should let you know if its hardware or software related, but it is a pain to do.
When experiencing tech problems, it's usually just a case of trial and error until you work out what the issue is.
Good Luck, let me know how you get on.