What steps will reproduce the problem?
1. Use the Attached "test" batch file 
2. Configure the tool in Pyscripter
            Caption=Test
        Description=Testing script
    ApplicationName=<script path>\pylint.bat
         Parameters=$[ActiveDoc-Name]
   WorkingDirectory=$[ActiveDoc-Path]
           ShortCut=16468
            Context=tcActivePythonFile
          SaveFiles=sfAll
      ParseMessages=TRUE
     ParseTraceback=TRUE
     MessagesFormat=$[FileName]:$[LineNumber]: 
3. Start PyScripter using "Edit with PyScripter"  
4. Run the tool
5. Open another file from *another directory* using "Edit with PyScripter"
6. Run the tool on the second file
7. Look at the full path

The tool's working directory is $[ActiveDoc-Path].   The script outputs a 
simulated error with just the filename of the parsed file.  It would appear 
that the base path for the full filename displayed in the messages window is 
that of the first file.  Which would break the "goto ability" of the editor 
when the message is double clicked on.   

What version of the product are you using? On what operating system?
PyScripter 2.4.1.0, Win XP Pro 32-bit, Limited user

Please provide any additional information below.

The reason for stumbling aross this behavior was in dealing with pylint.  
Setting the working directory allowed importing from modules in the same 
directory as target script, XOR Not setting the working directory allowed the 
double clicking of messages to work properly.  Forutanely, In this case there 
was an easy work around.  Setting --init-hook parameter with the value of 
"import sys; sys.path.append(r'$[ActiveDoc-Path]\')"