gDEBugger automatically sets the debug flags on for you if you use the clCreateProgramWithSource API function.
If you have created the program binaries in a previous run of your application and are loading them with clCreateProgramWithBinary, do note that:
1. Debugging will not work if that previous run was not done with gDEBugger, or was done with a different driver version.
2. Even if it does work, you will not have associated code, so you could only view variables and step through code lines you cannot see in Visual Studio.
The recommended way of working with gDEBugger is online compilation of OpenCL code, with clCreateProgramWithSource and clBuildProgram.
GPU Developer Tools Support