missing Path(in UNIX) when i launch a job on to unix machine using windows SSh

hi

i want run an unix application from a windows program/application.i am using SSH(command line version)to log on to a unix machine from windows. the application has to read a configuration file inorder to run. the configuration file .CFG is in bin in my home directory. but the application searches for .CFG in the root bin. what sould i do to overcome this?
when i open a ssh window and run this unix application it runs fine i.e it searches in the correct place for .CFG

your help is appreciated.

Are you logging in as root while using the command line version? This would cause the home directory to be set as root and your pwd would be the home directory (root's home directory).
If you are trying to read the configuration file without using the absolute path, your script/program will look for the file relative to the pwd. May be thats why you have this problem.