Thanks for sending the report. It looks like there may have been some server changes since you started using SpamSieve. There are some adjustments in the new public beta version (2.9.48b3) that I think will help.
As to the messages from your employer’s domain, it does not look like SpamSieve classified any good messages from the same address as spam twice. However, if you want to be sure that all messages from that domain are classified as good, you could create a rule in the Whitelist window for From (address) Ends With @domain.edu (substituting in the proper domain).