When freenet-9999 is installed it creates /var/freenet owned by root:root instead of freenet:freenet. This prevents the application from starting because it can't write to it's own work directory unless you run the daemon as root. Reproducible: Always Steps to Reproduce:
If you had a clean system (no freenet user, no /var/freenet), then the dir should be created with the right permssions with the freenet user as owner. Did you create a freenet user previously, did you have a very early version of the ebuild installed or existed /var/freenet before?
I tried a completely clean install and this time /var/freenet was owned by freenet:root. I tried to confirm the original behavior by uninstalling freenet without deleting the freenet user and this time it made /var/freenet owned by freenet:freenet.