I have 319 NEF files in my folder, but LRT is showing 635 files. Most of the files (but not all) are shown twice.

LRT Pro7.0 beta 12 Build 962

With such reports, please add the log (info menu / show log) after it happened.
This way I don't know nothing - not which system you are running on, not which version you are using. It's impossible to help.
When you open the "Bug Reports" Forum, at the top there is an instruction on how to efficiently report a finding.
Please check that out. This helps me to help you.