I had the same issue and contacted support. Mine ended up being a bad head unit. Here's what they told me to try first before coming to the conclusion of bad firmware in head unit.
If the controller has a green status light, but the modules are flashing, then there are three possible reasons for this:
A device module or cable is preventing your modules from communicating with the base unit.
Your configuration has become corrupted and needs to be fixed.
Your base unit could be having some hardware problems.
To determine if is is a device or cable that is causing the module not to communicate follow the steps bellow and inspect AquaBus cables and ports for discoloration and corrosion: (send pictures if not sure)
Remove all the AquaBus devices from the base unit (including the display screen).
Now reconnect only your Energy Bar to the base unit.
If it comes back up both Green status lights on the Apex base unit and the Energy Bar, If so proceed to step #6.
If the Energy Bar is still blinking yellow then try another cable and AquaBus port on the Energy Bar.
Connect the Display module (do the modules status light stay Green)
Now connect the next module you have.
If it comes up with a Green status light on the module then proceed to step #8
If the Module is still blinking yellow then try another cable and AquaBus port on the Modules.
Repeat steps #6 and #7 until you find the problematic device.
They also recommended to try logging in using apex.local and to download the apex browse utility tools.
Nothing worked.
Because the Apex Classic is older models, they told me it couldn't be repaired as the parts were not available. I purchased another used apex and my original eb8 and display worked with the "newer" head unit.