clock problems with bag files

Hi, I am experiencing some problems here with bag files. I am running simulations with a bag file, I set --clock and use_sim_time true and yes I get the WARNING message when trying to run some nodes. As you can see from the launch file below I am only using ROS, not Gazebo and only .cpp nodes. And the node which is not publishing any more is the one included in the "ekf_template.launch" file (way too long to be posted!) I did not explicitly set us_sim_time true within this launch file but it worked well for a while, should I? This launch file has been working for a while but not any more. The only thing I can think of is that I added some python nodes within the package and yet the py nodes are not included in the launch file. Would it be possible that any system update or any other system setting might have affected the clock behaviour? Thanks in advance Marcello