Package Configuration messed up after package reinstall or pfsense upgrade

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I have noticed this issue with pfSense for a long time. Several packages have issues when they are reinstalled or pfsense is upgraded. It seems their actual config files are not re-generated until you go into the package config, in the menus, in the web admin, and simply click 'Save' which will then re-generate the config.

Is this a pfSense issue or an issue specific to those packages?

The ones that I see commonly are:
darkstat
ntop
lcdproc-dev

And sometimes:
bandwithd

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Who do I need to report this to or what do I need to do to get this resolved?

Thanks!