The problem manifests itself like so:
# twadmin --create-polfile -S /usr/local/etc/site.key /usr/local/etc/twpol.txt
### Error: Rule already defined as a start or stop point of another rule.
### /usr/local/lib: Line number 241
### Exiting...
The policy file was not altered.
and can be fixed by commenting out line 241 in policy/twpol-Linux.txt.
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