When that happens to me it is usually because I am in a collection or have a filter on. Right clicking on an original and selecting Go to Folder in Library usually fixes it. From there, I can add the new HDR image to the collection if I want.
I chose images from my original folder but the the tone mapped image still did not appear.That does not happen when i use Nicks HDR
I had not used Photomatix for awhile. After you wrote, "the tone mapped image still did not appear" I tried it. It stuck the file in the wrong place! I went into the Photomatix View > Preferences > Files setting and tried both "Default directory for saving" settings. Now it is back on "Directory of Source files" and is working.
I don't know why it had to be reset, but it seems to have fixed it.
Which do you like better? NIK or Photomatix?