Glad you find the program useful. It's always cool to hear from people using it for different things.
Interesting, thanks for reporting the problem. I've not encountered or heard of anything like this.
What base map (in TopoFusion) are you using, or do you have other maps completely turned off?
I don't have a fix for the problem. Worst case you could send me the maps, but first I will try to recreate it with several overlapping maps.
Thanks.