I think I may know what is going on here.
I defined "Working directory:" as %(HOME)/apt_tests
When I run: "echo %rw", it shows:
/home/rbresali/slickopt//home/rbresali/apt_tests/
Instead of showing:
/home/rbresali/apt_tests
/home/rbresali/slickopt is the directory with my project files.
So SE is prepending the project directory into the working dir when I do not want it to. If I wanted that, I would have put %rp there.