Just as a quick additional to this - A lot of the time Flat feet are indeed the cause of such problems and I've found certainly that it is misdiagnosed (as fallen arches) and mismanaged in the vast majority of cases. Most Flat feet problems are not fallen arches but are simply due to an everted calcaneous an as such have the secondary effect of causing the longitudinal arch of the foot to disappear. Now Knowing that I find it scary that for almost every flatfoot problem is simply to prescribe arch supports - unless u happen to be uber flexible then the arch supports will simply cause pain and in some extreme cases can compound the problem further and cause damage - this is because a simple arch support in the case of an everted calcaneous will recreate your arch but will do absolutely nothing for the heel problem, which means your foot is being twisted further out of alignment (forefoot will end up in excess suppination with the calcaneous still everted = pain and damage)

Now taking that into account the answer is quite simple. I believe that in your case you would benefit from a pair of insoles with medial wedges added to the heel (3/4 length with MINIMAL arch support and probs about 10-15 degrees of medial wedging at the heels) this will essentially treat the cause and not the symptom. I not only speak as an orthotist who see's this just about every day but also as a patient! - my doctor tried for years to fix me flat feet with arch supports etc but all it did was cause pain and like yourself i found that particularly when I was active i got pain in my shins (sometimes my knees as well - Im Very flat footed lol) - After i finished my degree and started working i made myself a pair of insoles similar to what I've suggested for you and the pain has pretty much disappeared - even during sports etc. Thats just my suggestion based on the info you have given us but I'd strongly reccomend as others have that you get a full assessment first - the fast way to tell if u have everted calcaneous' is to stand straight with your back to a mirror - if the line of the back of your foot where the achilles tendon runs splays outwards at your heel then its a positive test and the problem is definitely not a fallen arch and is an everted calcaneous.

I agree with whats been said here 100% that you need to treat the biomechanical problem and not just try to get rid of the pain, and the above is how I'd go about it as an Orthotist but i know a vast number of podiatrists who treat numerous patients using the same rationalle with great success so it might be worth giving it a try in your case.

hope that maybe gives u another option to explore - although theres not a lot of literature on this particular subject but I will be happy to answer any questions you have