I had this issue myself and addressed it in a post (What happened to the Storm circles on my minimap?). I already tried deleting the storm controllers and starting over, but it did not fix the issue. Unfortunately, no one has found a fix or work-around yet, and I am starting to doubt we will get one for the current devices.
I heard some talk on the forums of a “V2 Devices” (THREAD: Community Concerns about V2 Devices) that was to be released in the near future (update 25.00, presumably in early June). I am suspecting that bugs in the current devices will not be fixed for a while if ever since they will most likely be made obsolete by the improved V2 devices.