"Good" messages are going into the Spam folder
Knowing precisely whether a message is Spam is difficult, particularly as spammers try to evade the various measures taken against them.
This means that sometimes the MailCOPA email client will misidentify innocent messages.
There is a simple way of finding out just what it was that caused the message to be identified as spam: right-click on the message in the message list and select Spam 
Display Spam Score. This will show the factors that contributed to the spam score, as well as the total spam score.
There are three ways of reducing this "over-eagerness":
1. Reduce the spam checking level - from the Configuration menu select Set Preferences and go to the Spam configuration page. Change the spam checking level value in the dropdown control.
2. Move the message to another folder (either by right-clicking the message in the Message List and selecting the appropriate option from the context menu, or by drag and drop). This will also add the sender's address to the white list - mail from addresses on this list will escape spam checking
3. Right click on the message in the message list and select Spam Learn as Clean. This will teach the Bayesian filter that this message is not SPAM.
One other common reason for good messages ending up in the Spam folder is because of user created filters. These will not show up in the spam score so can be confusing as the MailCOPA email program will report the message is not spam, but it still ended up in the spam folder.