When installing the FreePBX Distro, there is a step in the OS questions at the beginning that asks for your Time Zone. After the installation is complete, going to System Admin ------> Time Zone, the GUI reflects the choice made during the installation. Perhaps this is why many are considering it a problem. The question is asked and answered, but isn't actually applied in FreePBX.
No biggie though. Perhaps the updated version won't do this. But when users see the correct time zone in the GUI, but have the wrong time in Time Conditions, the problem will be brought up again.... and again... and again...