Are you talking about the "Error compass variance" error?
I've made some reseaching and found the following:
Remember the compass variance is caused by a difference in reported compass data between the two compass. The fc is not happy that it is getting very different data from the two compass. The most common problem is that one or both of the compass are not aligned to front correctly but it can be caused as you note by electromagnetic interference to one or both of the compass.
You just have to use the external or the internal compass or the gps will go crazy.