Ancestry.com knows they have this problem. I found it during beta testing that they let me do in 2011 and they refused to fix it. Instead they dumped it on the public. Like a dummy I transferred all of my family trees over to FTM 2012 and now whenever I try to merge files, the program stops working and shuts down! I cannot even merge 20 people!
I have finally given up all hope of getting this program to work correctly for me and I have been using various FTM programs since Ancestry.com first released them. I have over 100,000 people on my tree and I wish I would never have moved them to FTM 2012!