Do feet get BETTER?

I have for a long time had pretty flat feet and been a severe over-pronator. I have worn motion-control type shoes (Brooks Beast) to give my feet the proper support for about the last 3 years or so. Within the last 8 months, I have upped my level of training in order to start doing triathlons. I had no problems up through my first sprint race which was about a month ago.

Since that race, I have continued my training and just completed my second sprint race this past weekend. However, since my last race, I have been having more and more foot pain. This include plantar facia, knees, shin splints, ankles, etc. After doing this race, I had sever pain in the ankle the next day. It is starting to subside now that I have taken a couple days off.

My shoes are not new (neither the style nor this particular pair) and they are not worn out (probably about 100 miles on this pair) so I have ruled that out. My question is: Can it be that my form or ankle strength has improved with training and now the extra support in those shoes is too much for me, thus causing pain??

Anyone have any suggestions?? I have some longer run events coming up that I need to train for!