If you switch to barefoot/minimalist running you need to remember this is not for every body.
First, be careful not to be overweight as running without cushion will injure more easily your tendons around your feet and your knees.
Also, you should have less pain running barefoot/minimalist if you are already a forefoot runner. Running with this type of shoes will change drastically the way you use your feet when running and therefore, your calves will be used differently. I noticed calves pain when I first started running in Vibram - which I had to get used to at the beginning, and doing only very light running sessions (10min run, then rest, 20min run then rest, etc).
As for your question, if you have arch pain when running in "normal" trainers, I advise you to reinclude them in your training as you need to get used to it. I think this is the same type of issue kenyans have to face when they've been running since their early age barefoot and when they have to wear shoes to race.
A friend of mine used his vibram for every single run for over 2 years, he did a 10k with normal trainers and got his knee injured (tendonitis). Cannot conclude any link between using trainers and his injury, but looks like your problem a lot.
Conclusion:
- use your minimalist for every run and race and you might not get injured
- train with your normal trainers if you plan to use them in the future (such as for marathons, dont think minimalist will be best choice?)
Cheers