Are you using the same python initialization script as for LS1043ARDB and using the Connect flow as I depicted above? There are 2 possible reasons for not showing the flash devices in GUI:
1. If you're using different flash devices added via monitor commands that are not supported by us. See bellow:

2. If the monitor commands are not correctly used.
If you're using a different initialization file can you please share with us?
To have a clear conclusion (maybe there is a glitch in the FP GUI), please make a try also with the flash programmer support from gdb cmd line. Take a look in the chapter 7 (Flash Programmer) from Targeting Manual -> CW_ARMv8\ARMv8\Help\PDF to see how to use it. Is pretty simple (just make sure to terminate the connection from CW eclipse).
Thanks,
Marius