You are using an older version of Visual MODFLOW Flex, and I recommend reverting to the current one if possible as the charting part was significantly upgraded and improved.
It's hard to tell what may be missing here. Make sure you are saving outputs at every time step and also make sure that the simulation time interval is commensurate with your observation data. Observations must be added to the model prior to translating and running it. I remember that older versions of Flex sometimes had issues such as the one you encounter.and in most of the cases they could be attributed to data inconsistencies.