Running with Nike Free Runs...

Anyone can correct me if I'm wrong, but I think those shoes are more minimalist running shoes and if you're not used to running in them they'll make you sore cause you're not used to using those muscles. Since minimalist shoes are supposed to make you strike on your forefoot, that could explain why your arches hurt. You're just not used to it. It's kind of unrelated, but when I started dancing ballet, my arches would get so sore until those muscles developed.

Weebs is correct, they are minimalist shoes, so too much support should not be an issue. It is likely that they do not have as much support as you are used to.
When transitioning from a supportive shoe to a minimalist shoe, its a good idea to work up to it as they tend to use muscles that you aren't used to. That is likely why you are having issues.

I am not against minimal/barefoot running, however, it isn't always for everyone.
Keep in mind when buying running shoes, it doesn't matter how well a shoe works for others, it might not work for you.

If you feel that the minimalistic shoes are the way you want to go, then I would say try to do short runs (like a mile or so) in them every few days to build up the strength in your feet. But as a new runner you might want to stay with the more structured shoe for your runs. I've given up the Free's cause even when my feet got used to them the lack of cushioning and support made my legs and back hurt. Got much better when I went back to my regular shoes.

I just started using free runs also and experienced some of the same issues you are having especially the sore toes. I usually ran in Nike cross trainers and I played basketball in Nike basketball shoes. It makes sense that they are minimalist shoes because there is little support, however I have been running in them for about a month and the issues I had have gone away as I have broken them in. I had the arch problem only in my left foot, probably because I needed to develop the muscle in that leg. I also switched to a thinner dry fit sock instead of the thick cotton socks I used in my basketball sheos and cross trainers. I am running a 10k on Saturday and have been running that distance the past two weeks in them and I am honestly really liking them but they do take some getting used to especiallyon days when I play basketball and then run in the evenings.

I have always had supination of the foot, and high arches. After seven years of barefoot martial arts my feet were pretty strong so the transition into barefoot shoes was easy, and my arches have always held up. I have *never* had an issue with my arches. I eventually ended up with a pair of vibrams (the five finger kind) and they were the best running investment I've ever made.

I had to run in a pair of Nike frees v.2 for a 10k charity fun run three days ago (I was wearing a onsie with socks sewn onto the end of the legs, so basically I couldn't free my toes to slip my vibrams on). And lo and behold, I have for the first time in my life sustained an arch injury.

I began running seriously almost two years ago, and the nikes were my first shoe. I used them for a year before getting the vibrams. When I ran in them on Sunday, I felt as though the soles had actually been made on a slope, higher on the outside of the foot and lower on the arch, and that they were forcing my feet down onto their arches, forcing my ankles inward. Keep in mind I am used to running on a flat surface with a layer of rubber between my feet and the ground. Vibrams are as close to barefoot as you can get ( apart from maybe wearing just cotton socks).

So with this in mind, I'm gonna put this out there; I don't actually think nike free runs are very good for the arch of the foot. If I am as used to the barefoot style as I am, surely a padded shoe would be a welcome luxury, not abrasive and damaging? I'm not saying the arch of the foot needs support- quite the contrary, I think it just needs strengthening, with short distances of low impact running with no padding at all, and slowly building up distance. I genuinely believe the nike free runs have a sole which is imbalanced.

If the free runs are working for you I'm really glad, and keep with them because a running shoe that suits you is hard to find.

Old thread, but If you look up alternative ways to lace your shoes, it should help. I have hammer toes, so I lace my shoes so that the box part of the shoe (toe part) is lifted up. I also cut my toe nails every 2-4 weeks.