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What is the difference in the heel of the shoes you were wearing and the ones you switched to?
It may be too big of a difference all at once. Minimal shoes ask alot more out of ankle rom, heel cord, and posterior chain. It can take 2 or 3 progressions in shoes to get to a minimal shoe based on what you are coming from. Progression is key.
Another aspect to look into is your foot strength. With arch support etc. the shoe is making the correct for you vs your foot making the correction.
If you notice that you are walking on the outside of your foot this is something that needs attention. You want to walk on your entire foot always.
Yes incorrect walking or running patterns/technique will cause problems.
Is there someone with experience in teaching running technique at your gym or somewhere you have access to?
Have someone video tape you running so you can see exactly what you are doing vs what it feels like you are doing.
There are several running technique videos on CrossFit Endurance http://www.crossfitendurance.com/run
It would be very beneficial to attend an Endurance Seminar since running is the skill of focus. Attendees are video taped 2 time during the weekend and receive feedback. Drills are presented and done throughout the weekend. A list of scheduled seminars is found here http://www.crossfitendurance.com/blog/5