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It looks like you're sourcing the ros setup and workspace setup files in the wrong order.

source $ROS_WS/devel/setup.bash
source $ROS_KINETIC/setup.bash

The main ros setup.bash will overwrite the workspace setup, so you always want to source the workspace setup.bash file second.

It looks like you're sourcing the ros setup and workspace setup files in the wrong order.

source $ROS_WS/devel/setup.bash
source $ROS_KINETIC/setup.bash

The main ros setup.bash will overwrite the workspace setup, so you always want to source the workspace setup.bash file second.

Update thanks for the new information. There are two differences that look like they might be causing the problem. ROSLISP_PACKAGE_DIRECTORIES is blank when setup using 'env.sh' the other is that the order of the paths in ROS_PACKAGE_PATH is reversed. If i had to guess the missing ROSLISP path is looking the most suspicious.