Square brackets cannot be nested (E.G. "[a phrase;another phrase] [an optional phrase;]" is correct, "[a phrase;another phrase [an optional phrase;]]" is not)
Your current input generates these phrases:
All Not set bodies
All bodies
everything in this system have been scanned with the F S S
everything in this system have been scanned with the full spectrum scanner
everything in Not set have been scanned with the F S S
everything in Not set have been scanned with the full spectrum scanner
"Not set" is where your variable values would go.
You can check which phrases will be generated using
this command (as the syntax for dynamic command sections and dynamic responses is identical)
The corrected version would look something like this:
[All {INT:EDDI system scan complete count} bodies;All bodies;everything] in [this system;{TXT:System name (spoken)}] have been scanned [with the F S S;with the full spectrum scanner;]