The utility scripts included in POPFile v1.1.1 remove some entries of the configuration file.
Ex.
After running bayes.pl, popfile.cfg will be like:
GLOBAL_debug 1
GLOBAL_last_update_check 1265500800
GLOBAL_message_cutoff 100000
GLOBAL_msgdir messages/
GLOBAL_timeout 60
GLOBAL_update_check 0
bayes_bad_sqlite_version 4.0.0
bayes_corpus corpus
bayes_database popfile-sqlite3.db
bayes_dbauth
bayes_dbconnect dbi:SQLite:dbname=$dbname
bayes_dbuser
bayes_hostname ibook-g4.local
bayes_localhostname
bayes_nihongo_parser kakasi
bayes_sqlite_journal_mode delete
bayes_sqlite_tweaks 4294967295
bayes_subject_mod_left [
bayes_subject_mod_pos 1
bayes_subject_mod_right ]
bayes_unclassified_weight 100
bayes_xpl_angle 0
config_pidcheck_interval 0
config_piddir ./
history_archive 0
history_archive_classes 0
history_archive_dir archive
history_history_days 366
html_language Nihongo
logger_format default
logger_level 2
logger_logdir ./
The settings for the UI and Proxy modules are missing.
POPFile v1.1.0 does not have the problem.