Hi,
I'm sorry, I haven't been able to reproduce the problem with 'Internal error'.
However, the warnings that are shown in the tooltip "Device configuration is not supported..." only mean that these tools are not available because they require DCD and TrustZone modules that are not present on the LPC54606 microcotrollers. You can just ignore those warnings.
Does the problem with the "Internal error" message persist and is it always reproducible?
If so, could you please send me the log file that is located in the following folder:
c:\Users\{your user id}\.nxp\nxp_conf_workspace_v11.0\.metadata\.log
Regards
Petr Hradsky
Config Tools Team