If your application uses an application configuration file, e.g. myapp.exe.config, it won't be loaded by default when the fitSharp Runner executes. To specify the application configuration file, use the -a switch.

!define COMMAND_PATTERN {%m -a c:\mypath\myapp.exe.config
   -c c:\myfolder\mysuite.config.xml
   -r fitnesse.fitserver.FitServer,c:\program files\fitsharp\fit.dll %p}

or

c:\program files\fitsharp\runner -a c:\mypath\myapp.exe.config
   -c c:\myfolder\mysuite.config.xml
   -r fit.Runner.FolderRunner,c:\program files\fitsharp\fit.dll