Yes, I know, this thread is quite old, but I just had the same problem. I don't know if it's a dual monitor issue, but in a fresh installation on Windows 7 Ultimate x64, the Transformation Panel didn't show up no matter what I did. I searched the Registry for "TypeTool", and I found the entry HKEY_CURRENT_USER\Software\FontLab\TTool3\General\TransformationPosX with a value of 4294934528 (0xffff8000). Well, that's a bit bigger than any screen I could think of...

I shut down TypeTool, set the value to 1000 (0x000003e8), restarted TypeTool, and the Transformation Panel showed up again. I don't know what caused this problem. Maybe that my secondary monitor is placed to the left of the primary one - some programs seem to choke a bit on this setup.
Cheers,
Jan