To the OP,
I think I just solved my issue. Here are the links that solved it. I googled "Application popup: : \SystemRoot\System32\ATMFD.DLL failed to load" and I used the optional google translated link
http://www.51nb.com/forum/tid751535,1
http://translate.google.com/translate?hl=en&sl=zh-CN&u=http://www.51nb.com/forum/tid751535,1&ei=cdLPSejiGcWhngey6KjwDw&sa=X&oi=translate&resnum=8&ct=result&prev=/search%3Fq%3DApplication%2Bpopup:%2B%2B:%2B%255CSystemRoot%255CSystem32%255CATMFD.DLL%2Bfailed%2Bto%2Bload%26hl%3Den%26safe%3Doff%26newwindow%3D1
In my case, this problem happened on a T61 Thinkpad with NVIDIA Quadro NVS 140M display adapter and as stated I recently reformatted due to a new hard drive. I did grab all the latest drivers for my new hd and just now I reverted to the previous Nvidia video driver and upon rebooting and checking out event viewer, the app pop up message appears to be gone. The video drivers I had and reverted back to match the link's drivers. I'll update this thread if I get the message again but this appears to be the resolution for me. Hope that helps.