Ok so the problem is while collecting, not while importing and analyzing data, correct? I was commenting on the latter, sorry.
I think this is a Polhemus issue, either a hardware problem (likely) or wrong configuration (look at the volume it's trying to detect, only half the space around the emitter is in the acceptable zone). You can try testing it separately from Brainstorm. They have a software you can download. Please search for Polhemus on this forum, there was a very recent discussion about this that might help. Or contact Polhemus support.