Brian,
You can check HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\FLEXlm License Manager for LM_LICENSE_FILE. Also, you can download the latest Mentor Standard Licensing release and once it's installed, you can use the Start >All Programs > Mentor Graphics > Mentor Install then Manage Licensing > License Utilities > Manual Environment Editor to clean up the registry. Depending on the version and bit-width you're using for LMTOOLS, it may be pulling from and writing to different locations. The editor in the Mentor installer is an easy way to clean things up.
http://supportnet.mentor.com/portal?do=releases&prod=C106-S128-G159-P11292
Guy