It could be anything('navicular' is definitely not a problem confined to certain breeds, just more prevalent(or acute) in QH/arab type hoof confos) but I'd also guess it's probably bruising/sensitivity due to weak, unconditioned(to gravel) heels & just coming out of shoes. Sending us hoof pics of various angles would give us more ideas of specifics.
Don't just pray, but do some research & learn about hoof function & factors that affect soundness. Also there are a few different approaches and many different standards of 'expert' out there, so blind faith is not something I'd advocate - do your homework, so that you have an idea of which 'experts' really know what they're on about & are worth listening to & employing. On that note, hoofrehab.com & barefoothorse.com are great places to start. barehoofcare.com is another good one, which includes a section on considering situations in which metal shoes may be appropriate & least likely to have adverse effects.
I too would say boot/pad him for rough stuff, so you don't have to avoid it. Also interested how much & what sort of riding you do, and how long has he been shod for, considering he's still a youngster? I don't advocate putting metal shoes on a horse until they're mature, so their feet at least have a chance to develop properly first.