@jmon the expected path of the batch file is actually the B4J programs file folder.
For example mine is C:\Apps\B4J
So if I want to run myScript.bat (without pathing it) it would need to be in C:\Apps\B4J
I used Process Monitor to see what file B4J was trying to execute. What I have noticed is that if no path is specified then the space between the comma and the script name is included.
ie B4J was trying to call C:\Apps\B4J\ myScript.bat (there is a space between the last slash and the script name.
To solve this use remove the space;
#CustomBuildAction: 2,myScript.bat,
In your case .\myScript.bat then B4J will be looking in C:\Apps\B4J but you dont need the .\