Does anyone else have flat feet?

Stop working out until the pain stops or you know what the problem is. You have a probable serious or soon to be serious injury. Stay off the foot. Inserts or shoes aint gonna fix what ails ya.

Yep, OP, right now, you are in a state of injury, which needs to be dealt with before you even start looking at future exercise options. Anything you do now puts you at risk of increasing recovery time or doing permanent damage, depending on what the root of the problem is. As we are unable to diagnose your actual issue with certainty, it's not clear what treatment would be suitable. I would almost think that at least a round of physio may be necessary.

Once that's taken care of, you can start looking into maintenance/pre-requisite training to ensure you avoid a similar or related injury in future.

As for your knees, yes, they are strongly related to your arch height, ankle strength, etc. When you have collapsed arches, your feet pronate inwards (hence the traditional notion of shoving a motion control/orthotic object to prop up the arch), your ankles turn in, and your knees have uneven stresses applied. If you strengthen each of these points (strengthened arch muscles for better ability to rebound, stronger ankles to avoid wobbling, stronger muscles around the knees for side-to-side stability, core strength to stabilize forward/backward pelvic tilt), your tendons and soft tissues will no longer be subjected to stress/tension in dimensions in which they were never intended to move under "correct" operation.

When you say you lift heavy, what exactly are you doing? I have read, for example, that women tend to have disproportionately strong quads compared to hamstrings. During squats, if you don't squat low enough until the hamstrings are engaged, you can wind up further increasing the front/back imbalance. It could be one case of how one could be prone to joint injury despite having quite muscular legs.

But yes, try to at least keep stress on your feet to a minimum to see if the pain subsides a bit. Ideal would to find a way to seek medical attention just in case you need surgery or something.

I'm getting there because I wear Converse. I would see a doctor. They probably can lead you to the right shoe or inserts.

Flat feet. The forty intrinsic foot muscles that have been cushioned,supported and braced (http://www.merriam-webster.com/dictionary/orthotic ) which are responsible for your arch are now in an atrophied dysfunctional state. Permanent bracing of dysfunction ,injured, deformed muscles or joints was abandoned in the early 1900" in all other areas of medicine.You corrected stated that everything is connected. Just like any other structure you would never correct a crack in the fourth floor/knees ,sixth floor/lower back or 11th floor/shoulders without fixing the foundation first. When the foot flattens the knees twist in, one hip drops and one shoulder drops in the opposite direction. Walking barefoot in the sand or grass will rehabilitate your foot muscles. This is why only 3% of unshod populations seek medical help for foot,knee and back problems. When you are wearing shoes you need to wear the Barefoot Science non- orthotic insoles. Once you have progressed up to level three of the BFS system you should switch to a flat ,flexible shoe. There are over 100 muscles, tendons and bones in the feet and they will not operate efficiently if they are restricted, cushioned, braced or supported. Period. You will have injuries for your entire life if you do not fix the foundation and align the skeletal system.
The amazing results that have come to the surface through SEMG testing is that soon as you initiate the foot's proprioceptors the entire gait related musculature records a 30+% increase in activation of the peronous longus, Anterior tibiallis(lower leg) , knee, hamstring, glute and paraspinal muscle groups and a 40% increase in balance and stability. This increase in muscle efficiency instantly completes the upright posture circuit which levels the pelvis without effort. It amazes me when I hear that people have been convinced to have surgery on their feet before do anything to rehabilitate them. Why would anyone think that they should be born with strong muscular feet when coming out without a six pack, rippling biceps or chest is acceptable.
As a soon as you stop treating the feet like a bag of bones at the end of your body and include them in your daily exercise and stretching routine all of your problems will disappear.
http://www.barefoot-science.com/proof Guaranteed!
http://www.toesalad.com/reviews/a-review-of-the-barefoot-science-foot-strengthening-system/

Hope this helps.

I have a pair of arch supports that were made to fit my feet when I was in my early teens and I still wear them to this day. I can wear them in just about every pair of shoes I own, except my sandals. A couple of years ago I tried the Dr. Scholls inserts but they didn't give me as my support so I went back to my good old ones that were made for my feet. I think I will cry the day that I have to finally retire them.

I have flat feet also and then my kids may them even flatter. My pain is in my heel though, not my toes. I have a Wii Fit and my center of balance is where I put too much pressure on my heels. I bet if you tried one out you would be my opposite. Believe it or not my chiropractor makes my feet feel so much better. It sounds weird to say my Dr. adjusts my feet but the pain was so awful I hobbled, not walked.
I also make sure that my shoes have arches and wedges are my best friend. When I work out I wear Reeboks recommended by the employees at the shoe store for arch support and Dr Scholl's gel inserts. They feel so nice on my feet. For athletic shoes, it was worth it to pay the extra money and go to an athletic store as they know their product line better than a department store.

I am 41 and have dealt with flat foot problems most of my life. I have used custom-made orthotics, inserts from the store shelf, etc. As far a shoes go, the most comfortable for my feet are the Boombah Reverence training shoes. They are very comfortable and I have worn them for several years now without inserts.