Just stick with it and work closely with your command. You will need that CO recommendation, no doubt, and it needs to find its way into the potential block of your OER.
It doesn't really matter what unit you are at as long as your command gives you a recommendation. I would pick a unit that puts you in a career track that would be something you would enjoy in the event you don't get flight school. Also, normally if you are doing a job you enjoy it will translate to good performance and marks.
In all my years of aviation, I have never met anyone medically qualified that didn't get picked up for flight school that continuously applied every 6 months. I'm sure they are out there, but I've never heard of them. Persistence pays off so apply when you are ready and if you don't get it, KEEP APPLYING!